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Endangered Species Act - Section 7 Consultation

BIOLOGICAL OPINION

06E11000-2014-F-0078

For

Bull Trout and Bull Trout Critical Habitat

From

Thompson River East—Bridge and Approaches

STPP 6-1(87)56; CN 4039

2014

Agency: Federal Highways Administration

Montana District

Helena, Montana

Consultation Conducted by: U.S. Fish and Wildlife Service

Montana Field Office

Helena, Montana

Date Issued: February 19, 2014

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Table of Contents

I. Introduction and Consultation History 3

II. Description of the Action 3

III. Analytical Framework for the Jeopardy and Adverse Modification Determinations 6

IV. Status of the Species and Critical Habitat 10

V. Environmental Baseline 26

VI. Effects of the Action 29

VII. Cumulative Effects 36

VIII. Conclusion 37

INCIDENTAL TAKE STATEMENT 38

References Cited 45

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I. Introduction

This biological opinion addresses project related effects to the threatened bull trout (Salvelinus

confluentus) and bull trout critical habitat in accordance with the Endangered Species Act (Act)

of 1973, as amended (16 U.S.C. 1531 et seq.). The Federal Highways Administration

(Administration) and the Montana Department of Transportation (Department) are proposing to

replace a bridge over the Thompson River and to reconstruct the highway approaches near the

bridge. The U.S. Fish and Wildlife Service (Service) based this opinion on our review of the

Administration’s Biological Assessment for the Department’s Thompson River East—Bridge

and Approaches (STPP 6-1(87)56; CN 4039) project and on additional information in our files.

Section 7(b)(3)(A) of the Act requires that the Secretary of Interior issue biological opinions on

federal agency actions that may affect listed species or critical habitat. Biological opinions

determine if the action proposed by the action agency is likely to jeopardize the continued

existence of listed species or destroy or adversely modify critical habitat. Section 7(b)(3)(A) of

the Act also requires the Secretary to suggest reasonable and prudent alternatives to any action

that is found likely to jeopardize the continued existence of listed species or result in an adverse

modification of critical habitat, if any has been designated.

This biological opinion addresses only the impacts to the federally listed bull trout and bull trout

critical habitat within the action area and does not address the overall environmental

acceptability of the proposed action.

Consultation History: On December 11, 2013 the Service received a biological assessment

(MDT 2013) from the Administration for review and a request to initiate formal consultation for

effects on the threatened bull trout and bull trout critical habitat from the proposed Thompson

River East—Bridge and Approaches project (STPP 6-1(87)56; CN 4039) in Sanders County,

Montana. On December 17, 2013 the Service sent an email request for additional information

pertaining to the biological assessment. On December 23 and 24, 2013, the Department

responded to the Service’s prior email with additional information that further clarified details in

the biological assessment.

The proposed action will occur in the Lower Clark Fork core area and in the Clark Fork River

Basin Critical Habitat Unit 31 (CHU), Lower Clark Fork River Critical Habitat Sub-unit

(CHSU). This CHSU is part of the larger Clark Fork Basin CHU and is essential to conserving

the Interim Recovery Unit (USDI 2009a p. 33). The proposed action would affect bull trout that

occupy the Thompson River and its designated critical habitat.

II. Description of the Proposed Action

The action area is defined as all areas to be affected directly or indirectly by the federal action

and not merely the immediate area involved in the action (50 CFR 402.02). The action area for

this biological opinion is the portion of the Thompson River 600 feet upstream of the proposed

bridge replacement, and approximately 1,300 feet downstream to the confluence of the

Thompson River with the Clark Fork River. This upstream area is based on the approximate

distance that the Service expects bull trout to detect and respond to noise from proposed blasting

that would blast the center truss off of the piers, and the area downstream is based on the portion

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of the Thompson River that could be temporarily affected by physical obstructions from the

existing structure once it is dropped off of its piers, possibly into the channel.

The following description of the proposed action is taken from the amended biological

assessment (MDT 2013 pp. 3-4, 15-16):

The proposed project is located in Section 18 of Township 21 North, Range 28 West of Sanders

County, approximately 5 miles east of the city of Thompson Falls, MT on Highway 200

beginning at Reference Post (RP) 55.9± and extending eastward 0.9+ miles to RP 56.9±. The

proposed action would replace the bridge over the Thompson River at RP 56.3 and reconstruct

the highway approaches in the vicinity of the bridge. The existing bridge is a deck truss bridge

built in 1935 and is functionally obsolete and eligible for replacement. A new bridge would be

built on an offset alignment and the roadway approaches would be reconstructed to tie in with

the highway. This project is located at approximately river mile 0.3.

The existing 5-span bridge is 428 feet long and 24 feet wide. It spans a 100 foot deep chasm of

the Thompson River about 1,300 feet upstream of its confluence with the Clark Fork River. The

existing bridge is proposed to be replaced with a 3-span welded girder bridge 438 feet long and

40 feet wide. The new bridge centerline would be 40 feet north and parallel to the existing bridge

which would allow the entire bridge to be built while traffic remains on the old structure. The

new bridge design would eliminate any permanent construction within the 100-year floodplain

and wildlife movement underneath the new bridge would be sustained. Temporary construction

impacts to the wetted surface of the Thompson River may occur as a temporary work bridge

upstream of the new structure may likely be required in order to place new beams and provide

access for drill rigs associated with drilling the drilled shafts for the new bridge piers. Demolition

of the existing structure would most likely require minor blasting of the center truss off of the

piers and dropping it into or over the river. A crane would then pick sections of the bridge up as

they are cut by construction workers. At this point, within 3-5 days, the structure could be lifted

and cut apart and hauled out of the construction zone. Demolition of the existing piers would

likely involve an excavator with a hammer to break the piers into pieces. Positive catchment on

the river side would likely be placed to prevent excess rubble from rolling into the Thompson

River given adjacent slopes. The second possible demolition method could involve the contractor

installing another short work bridge downstream of the existing structure to lift and cut the

existing structure. This methodology would be slow, require more temporary pilings in the river,

longer duration of instream work and result in more disturbance to the adjacent riparian area.

Conservation Measures: The proposed construction of the new bridge and rip-rap drainage

chutes on the north side of the highway, along the upper east and west banks are not anticipated

to require any work below the Ordinary High Water mark of the Thompson River. However,

conservation measures are warranted to minimize the likelihood of impacting bull trout and bull

trout critical habitat. The conservation measures that will be employed by the proposed action

include:

1. In-stream work would be kept to the absolute minimum amount necessary. No

construction equipment would be allowed to operate within the active channel of any

stream unless otherwise permitted to do so (e.g., U.S. Army Corps of Engineers,

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Montana Stream Protection Act 124 Permit). When feasible, schedule in-stream

construction activities such that as many of the necessary construction activities as

practical occur “in the dry” or during low flows. Complete in-stream work

expeditiously in the shortest amount of time possible.

2. To the maximum extent practical, the existing bridge will be disassembled and

removed. If portions of the existing bridge are dropped into the stream during

demolition, they will be removed from the stream without dragging the material along

the streambed. Any blasting required for removal will be contained to the maximum

extent possible using some type of containment or shielding device to prevent debris

from entering the stream.

3. Best management practices for erosion control were applied to these projects,

including:

a. using acceptable erosion control measures to prevent sediment from reaching

water bodies;

b. using acceptable erosion control measures in borrow ditches to prevent erosion

and sediment transport into adjacent streams or wetlands;

c. quickly reseeding and revegetating all disturbed areas with desirable vegetation,

including embankments and borrow ditches;

d. stabilizing disturbed channel banks; and

e. maintaining and protect riparian vegetation to the maximum extent possible

within the construction zones.

4. All waste fuels, lubricating fluids, herbicides, and other chemicals will be collected

and disposed of in a manner that ensured that no adverse environmental impacts

would occur. Construction equipment will be inspected daily to ensure hydraulic, fuel

and lubrication systems are in good condition and free of leaks to prevent these

materials from entering any stream. Vehicle servicing and refueling areas, fuel

storage areas, and construction staging and materials storage areas will be sited a

minimum of 50 feet (15 m) from ordinary high water, typically referred to as the Q2

elevation, wetlands, and contained properly to ensure that spilled fluids or stored

materials do not enter any stream or wetland.

5. Structures designed to minimize sediment and pollutant runoff from sensitive areas

such as settling ponds, vehicle and fuel storage areas, hazardous materials storage

sites, and erosion control structures, will be visually monitored daily, especially

following precipitation events, to ensure these structures are functioning properly.

6. The new bridge has been designed to prevent stormwater runoff including, de-icing

chemicals, road debris and sanding materials from directly entering the Thompson River.

Following the completion of construction, all stormwater runoff will be directed off the

bridge deck to locations beyond the bridge ends into vegetated swales and/or riprap

chutes that will allow for the filtration and removal of materials that may be detrimental

to aquatic life before it enters the Thompson River.

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7. Contractor will prepare and submit a Storm Water Pollution Prevention Plan (SWPPP) to

the Montana Department of Environmental Quality (DEQ) in compliance to the Montana

Pollution Discharge Elimination System (MPDES) regulations prior to construction

activities.

8. The Department’s contractor is responsible of the installation of acceptable erosion

control devices and BMP’s along the edges of rivers/streams and wetlands, and other

waters of the US prior to the implementation of any construction activities within the

project area. The Department or its contractor will conduct inspections of erosion control

devices as required by the General Permit for Storm Water Discharges Associated with

Construction Activity issued by the Montana DEQ. The inspections will continue until

vegetation has been re-established within the disturbed areas.

9. Upon locating dead, injured or sick bull trout, notification was to be made within 24

hours to the Service’s Montana Field Office at (406)449-5225. Information was to be

recorded relative to the date, time and location of dead or injured bull trout when

found, and possible cause of injury or death of each fish and provide this information

to the Service.

III. Analytical Framework for the Jeopardy and Adverse Modification Analysis

Jeopardy Determination: In accordance with policy and regulation, the jeopardy analysis in this

biological opinion relies on four components: (1) the Status of the Species, which evaluates the

bull trout’s range-wide condition, the factors responsible for that condition, and its survival and

recovery needs; (2) the Environmental Baseline, which evaluates the condition of the bull trout

in the action area, the factors responsible for that condition, and the relationship of the action

area to the survival and recovery of the bull trout; (3) the Effects of the Action, which determines

the direct and indirect impacts of the Federal action and the effects of any interrelated or

interdependent activities on the bull trout; and (4) Cumulative Effects, which evaluates the effects

of future, non-Federal activities in the action area on the bull trout.

In accordance with policy and regulation, the jeopardy determination is made by evaluating the

effects of the federal action in the context of the bull trout’s current status, taking into account

any cumulative effects, to determine if implementation of the action was likely to cause an

appreciable reduction in the likelihood of both the survival and recovery of the bull trout in the

wild.

Interim recovery units were defined in the final listing rule for the bull trout for use in

completing jeopardy analyses. Pursuant to Service policy, when an action impairs or precludes

the capacity of a recovery unit from providing both the survival and recovery function assigned

to it, that action may represent jeopardy to the species. When using this type of analysis, the

biological opinion describes how the action affects not only the recovery unit’s capability, but

the relationship of the recovery unit to both the survival and recovery of the listed species as a

whole.

The jeopardy analysis for the bull trout in this biological opinion uses the above approach and

considers the relationship of the action area and core area (discussed below under the Status of

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the Species section) to the recovery unit and the relationship of the recovery unit to both the

survival and recovery of the bull trout as a whole as the context for evaluating the significance of

the effects of the Federal action, taken together with cumulative effects, for purposes of making

the jeopardy determination.

Adverse Modification Determination: This biological opinion does not rely on the regulatory

definition of “destruction or adverse modification” of critical habitat at 50 CFR 402.02. Instead,

we have relied upon the statutory provisions of the Act to complete the following analysis with

respect to critical habitat.

In accordance with policy and regulation, the adverse modification analysis in this biological

opinion relies on four components: (1) the Status of Critical Habitat, which evaluates the range-

wide condition of designated critical habitat for the bull trout in terms of primary constituent

elements (PCEs), the factors responsible for that condition, and the intended recovery function of

the critical habitat overall; (2) the Environmental Baseline, which evaluates the condition of the

critical habitat in the action area, the factors responsible for that condition, and the recovery role

of the critical habitat in the action area; (3) the Effects of the Action, which determines the direct

and indirect impacts of the proposed Federal action and the effects of any interrelated or

interdependent activities on the PCEs and how that will influence the recovery role of affected

critical habitat units or sub-units; and (4) Cumulative Effects, which evaluates the effects of

future, non-Federal activities in the action area on the PCEs and how that will influence the

recovery role of affected critical habitat units.

For purposes of the adverse modification determination, the effects of the federal action on bull

trout critical habitat are evaluated in the context of the range-wide condition of the critical

habitat, taking into account any cumulative effects, to determine if the critical habitat range-wide

would remain functional (or would retain the current ability for the PCEs to be functionally

established in areas of currently unsuitable but capable habitat) to serve its intended recovery

role for the bull trout.

The analysis in this biological opinion places an emphasis on using the intended range-wide

recovery function of bull trout critical habitat, especially in terms of maintaining and/or restoring

viable core areas, and the role of the action area relative to that intended function as the context

for evaluating the significance of the effects of the federal action, taken together with cumulative

effects, for purposes of making the adverse modification determination.

This analytical framework relies heavily on the importance of core area bull trout populations to

survival and recovery of the species. Core areas form the building blocks that provide for

conserving bull trout evolutionary legacy as represented by the major evolutionary groups

(Coastal, Snake River, and Upper Columbia River). Should the adverse effects of a proposed

action not rise to the level where it appreciably reduces both survival and recovery of the species

at a lower scale, such as the local or the core population, by deduction the proposed action would

not jeopardize bull trout at the higher scale of the interim recovery unit (Columbia River) or the

coterminous United States (i.e., range wide). Therefore, the determination would result in a no-

jeopardy finding. However, should a proposed action produce adverse effects that are

determined to appreciably reduce both survival and recovery of the species at a lower scale of

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analysis, then further analysis is warranted at the next higher scale. “Generally, if a proposed

federal action is incompatible with the viability of the affected core area population(s), inclusive

of associated habitat conditions, a jeopardy finding is considered to be warranted because of the

relationship of each core area population to the survival and recovery of the species has a whole

(70 CFR 56258).”

Survival is defined as the condition in which a species continues to exist into the future while

retaining the potential for recovery. This condition is characterized by a species with a sufficient

population, represented by all necessary age classes, genetic heterogeneity, and number of

sexually mature individuals producing viable offspring, which exists in an environment

providing all requirements for completion of the species' entire life cycle, including

reproduction, sustenance, and shelter. Recovery is defined as improvement in the status of listed

species to the point at which listing is no longer appropriate under the criteria set out in section

4(a)(1) of the Act. [50 CFR §402.02]. For the purposes of bull trout recovery, an emphasis is

placed on the adult (migratory) life history forms. Benefits of migratory bull trout include

greater fecundity resulting in increased reproductive potential, and dispersing the population

across space and time so that spawning streams may be recolonized should local populations

suffer a catastrophic loss (Rieman and McIntyre 1993, MBTSG 1998, Frissell 1999). In the

absence of the migratory bull trout life form, isolated populations cannot be replenished when

disturbance makes local habitats temporarily unsuitable, the range of the species is diminished,

and the potential for enhanced reproductive capabilities are lost (Rieman and McIntyre 1993).

The term conservation means the terms "conserve," "conserving" and "conservation" mean to use

and the use of all methods and procedures which are necessary to bring any endangered species

or threatened species to the point at which the measures provided pursuant to [the] Act are no

longer necessary. Such methods and procedures include, but are not limited to, all activities

associated with scientific resources management such as research, census, law enforcement,

habitat acquisition and maintenance, propagation, live trapping, and transplantation, and, in the

extraordinary case where population pressures within a given ecosystem cannot be otherwise

relieved, may include regulated taking. [ESA §3(3)]

In summary, the scales of analysis are as follows; local population, core area, management unit,

and interim recovery unit for the purposes of consultation and recovery. The core area scale is

an appropriate unit of analysis by which threats to bull trout and recovery should be measured

(FR 70, No 185). Similarly the geographical scales for critical habitat are as follows; stream

segment or water body, CHSU, CHU and the range of bull trout. Generally in the Clark Fork

Management Unit, core areas are similar in geographical scale to CHSU. The action will affect

the Lower Clark Fork core area and Lower Clark Fork CHSU. For the purposes of this

biological opinion all designated critical habitat supports and is occupied by a local population.

These relationships and scales of analyses are illustrated in Tables 1 and 2 below.

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Table 1. Hierarchy of units of analysis for bull trout jeopardy analysis for this biological

opinion. Local populations affected by the action are italicized.

Name/Units of scale Hierarchical Relationship

Coterminous United States Range of bull trout

Columbia River Interim Recovery

Unit/DPS

One of 5 Interim Recovery Units in the range of

the species within the coterminous United States.

Clark Fork Management Unit One of 23 Management Units in the Columbia

River Interim Recovery Unit/DPS

Lower Clark Fork Core Area One of the 36 core areas within the Clark Fork

Management Unit.

Local Populations: Bull River, Rock Creek,

Graves Creek, Prospect Creek, Vermilion

River, Fishtrap Creek, West Fork

Thompson River, Post Creek, Mission

Creek, Dry Creek, North Fork Jocko River,

Middle Fork Jocko River, South Fork

Jocko River, and Jocko River.

The closest local populations to the project site

are Fishtrap Creek and West Fork Thompson

River.

Table 2. Hierarchy of units of analysis for bull trout adverse modification analysis for this

biological opinion. Critical habitat segments affects by the action are italicized .

Name/Units of scale Hierarchical Relationship

Coterminous United States Range of bull trout/Critical Habitat 32 Units

Clark Fork River Basin Unit 31 One of 32 Units, defined as essential for the

survival and recovery of the species across the

range of the species. Based on the seven

guiding principles for the conservation (USDI

2009a p.1-3).

Lower Clark Fork Sub-Unit One of 11 Sub-Units within the Clark Fork

Basin Unit. This Sub-Unit is essential for

conservation of the species as one of the several

occupied major watershed in the Clark Fork

Basin Critical Habitat Unit.

Designated Stream Segments and Water

Bodies: Cabinet Gorge Reservoir,

McDonald Lake, Mission Reservoir, Noxon

Rapids Reservoir, Saint Mary’s Lake, Clark

Fork River, Cooper Gulch, Crow Creek, Dry

Lake Creek, East Fork Bull River, East Fork

Crow Creek, Fishtrap Creek, Flathead River,

Graves Creek, Jocko River, Mission Creek,

North Fork Jocko River, Post Creek,

Prospect Creek, Rock Creek, South Fork Bull

River, South Fork Jocko River, Swamp

Creek, Thompson River, Vermilion River,

West Fork Fishtrap Creek, West Fork

Thompson River.

These water bodies contain the habitats that

support local populations that in turn support

the conservation of the species for this CHSU,

CHU, core area, and Interim Management Unit.

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The draft Bull Trout Recovery Plan identifies the Lower Clark Fork core area as a primary core

area (USDI 2002b, pp. 131-132). In this Management Unit, a distinction has been made between

two types of core areas (primary and secondary core areas) based on the size, connectedness, and

complexity of the associated watershed and the degree of natural population isolation. The loss

of a primary core area would represent a significant gap in the range of the species within this

Management Unit. The following have been designated as primary core areas under recovered

conditions in the Clark Fork Management Unit: the Upper Clark Fork, Rock Creek, Blackfoot,

Bitterroot, Lower Clark Fork, Lake Pend Oreille, Priest Lakes and Priest River, Flathead Lake,

Swan Lake, and Hungry Horse Reservoir.

The Clark Fork River Basin CHU is essential for maintaining bull trout distribution within the

unique geographic region of the Columbia Headwaters Recovery Unit in large part because it

represents the evolutionary heart of the migratory adfluvial bull trout life history form (USDI

2009a p.32).

The Lower Clark Fork CHSU is essential to bull trout conservation because it provides an

important portion of the spawning and rearing habitat for Lake Pend Oreille, as well as an

essential migratory corridor for bull trout from Lake Pend Oreille to be able to access productive

watersheds upstream of this CHSU. Historic fragmentation of the CHSU due to three privately

owned mainstem hydroelectric dams (Cabinet Gorge, Noxon Rapids, and Thompson Falls)

seriously compromised access and productivity of this habitat for bull trout for nearly a century.

However, ongoing fish passage efforts (both fishways nad trap and transport programs) have

improved the longer-term prognosis for bull trout connectivity, and this CHSU is expected to

provide a critical linkage to recovering bull trout in the entire Clark Fork River CHU in the

future (USDI 2009a, p. 33; USDI 2009b, p.22).

IV. Status of the Species and Critical Habitat

This section presents information about the regulatory, biological, and ecological status of the

bull trout that provides context for evaluating the significance of probable effects caused by the

action.

A. Status of the Species

A.1 Listing Status

The coterminous United States population of the bull trout was listed as threatened on November

1, 1999 (64 FR 58910). The threatened bull trout occurs in the Klamath River Basin of south-

central Oregon, the Jarbidge River in Nevada, north to various coastal rivers of Washington to

the Puget Sound, east throughout major rivers within the Columbia River Basin to the St. Mary-

Belly River, and east of the Continental Divide in northwestern Montana (Cavender 1978, pp.

165-166; Bond 1992, p. 4; Brewin and Brewin 1997, pp. 209-216; Leary and Allendorf 1997, pp.

715-720). The Service completed a 5-year Review in 2008 and concluded that the bull trout

should remain listed as threatened (Fish and Wildlife Service 2008, p. 53).

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The bull trout was initially listed as three Distinct Population Segments (DPSs) (63 FR 31647, 64

FR 17110). The preamble to the final listing rule for the United States coterminous population

of the bull trout discusses the consolidation of these DPSs, plus two other population segments,

into one listed taxon and the application of the jeopardy standard under section 7 of the Act

relative to this species (64 FR 58930):

“Although this rule consolidates the five bull trout DPSs into one listed taxon, based on

conformance with the DPS policy for purposes of consultation under section 7 of the Act, we

intend to retain recognition of each DPS in light of available scientific information relating to

their uniqueness and significance. Under this approach, these DPSs will be treated as interim

recovery units with respect to application of the jeopardy standard until an approved recovery

plan is developed. Formal establishment of bull trout recovery units will occur during the

recovery planning process.”

Please note that consideration of the above recovery units for purposes of the jeopardy analysis is

done within the context of making the jeopardy determination at the scale of the entire listed

species in accordance with Service policy (Fish and Wildlife Service 2006, pp. 1-2).

Though wide ranging in parts of Oregon, Washington, Idaho, and Montana, bull trout in the

interior Columbia River basin presently occur in only about 45 percent of the historical range

(Quigley and Arbelbide 1997, p. 1177; Rieman et al. 1997, p. 1119). Declining trends due to the

combined effects of habitat degradation and fragmentation, blockage of migratory corridors,

poor water quality, angler harvest and poaching, entrainment into diversion channels and dams,

and introduced non-native species (e.g., brook trout, Salvelinus fontinalis) have resulted in

declines in range-wide bull trout distribution and abundance (Bond 1992, p. 4; Schill 1992, p. 40;

Thomas 1992, pp. 9-12; Ziller 1992, p. 28; Rieman and McIntyre 1993, pp. 1-18; Newton and

Pribyl 1994, pp. 2, 4, 8-9; Idaho Department of Fish and Game in litt. 1995, pp. 1-3). Several

local extirpations have been reported, beginning in the 1950s (Rode 1990, p. 1; Ratliff and

Howell 1992, pp. 12-14; Donald and Alger 1993, p. 245; Goetz 1994, p. 1; Newton and Pribyl

1994, p. 2; Berg and Priest 1995, pp. 1-45; Light et al. 1996, pp. 20-38; Buchanan and Gregory

1997, p. 120).

Land and water management activities such as dams and other diversion structures, forest

management practices, livestock grazing, agriculture, road construction and maintenance,

mining, and urban and rural development continue to degrade bull trout habitat and depress bull

trout populations (Fish and Wildlife Service 2002a, p. 13).

A.2 Species Description

Bull trout (Salvelinus confluentus), member of the family Salmonidae, are char native to the

Pacific Northwest and western Canada. The bull trout and the closely related Dolly Varden

(Salvelinus malma) were not officially recognized as separate species until 1980 (Robins et al.

1980, p. 19). Bull trout historically occurred in major river drainages in the Pacific Northwest

from the southern limits in the McCloud River in northern California (now extirpated), Klamath

River basin of south central Oregon, and the Jarbidge River in Nevada to the headwaters of the

Yukon River in the Northwest Territories, Canada (Cavender 1978, p. 165-169; Bond 1992, p. 2-

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3). To the west, the bull trout’s current range includes Puget Sound, coastal rivers of British

Columbia, Canada, and southeast Alaska (Bond 1992, p. 2-3). East of the Continental Divide

bull trout are found in the headwaters of the Saskatchewan River in Alberta and the MacKenzie

River system in Alberta and British Columbia (Cavender 1978, p. 165-169; Brewin and Brewin

1997, pp. 209-216). Bull trout are wide spread throughout the Columbia River basin, including

its headwaters in Montana and Canada.

A.3 Life History

Bull trout exhibit resident and migratory life history strategies throughout much of the current

range (Rieman and McIntyre 1993, p. 2). Resident bull trout complete their entire life cycle in

the streams where they spawn and rear. Migratory bull trout spawn and rear in streams for one

to four years before migrating to either a lake (adfluvial), river (fluvial), or, in certain coastal

areas, to saltwater (anadromous) where they reach maturity (Fraley and Shepard 1989, p. 1;

Goetz 1989, pp. 15-16). Resident and migratory forms often occur together and it is suspected

that individual bull trout may give rise to offspring exhibiting both resident and migratory

behavior (Rieman and McIntyre 1993, p. 2).

Bull trout have more specific habitat requirements than other salmonids (Rieman and McIntyre

1993, p. 4). Watson and Hillman (1997, p. 248) concluded that watersheds must have specific

physical characteristics to provide habitat requirements for bull trout to successfully spawn and

rear. It was also concluded that these characteristics are not necessarily ubiquitous throughout

these watersheds resulting in patchy distributions even in pristine habitats.

Bull trout are found primarily in colder streams, although individual fish are migratory in larger,

warmer river systems throughout the range (Fraley and Shepard 1989, pp. 135-137; Rieman and

McIntyre 1993, p. 2 and 1995, p. 288; Buchanan and Gregory 1997, pp. 121-122; Rieman et al.

1997, p. 1114). Water temperature above 15°C (59°F) is believed to limit bull trout distribution,

which may partially explain the patchy distribution within a watershed (Fraley and Shepard

1989, p. 133; Rieman and McIntyre 1995, pp. 255-296). Spawning areas are often associated

with cold water springs, groundwater infiltration, and the coldest streams in a given watershed

(Pratt 1992, p. 6; Rieman and McIntyre 1993, p. 7; Rieman et al. 1997, p. 1117). Goetz (1989,

pp. 22, 24) suggested optimum water temperatures for rearing of less than 10°C (50°F) and

optimum water temperatures for egg incubation of 2 to 4°C (35 to 39°F).

All life history stages of bull trout are associated with complex forms of cover, including large

woody debris, undercut banks, boulders, and pools (Goetz 1989, pp. 22-25; Pratt 1992, p. 6;

Thomas 1992, pp. 4-5; Rich 1996, pp. 35-38; Sexauer and James 1997, pp. 367-369; Watson and

Hillman 1997, pp. 247-249). Jakober (1995, p. 42) observed bull trout overwintering in deep

beaver ponds or pools containing large woody debris in the Bitterroot River drainage, Montana,

and suggested that suitable winter habitat may be more restrictive than summer habitat. Bull

trout prefer relatively stable channel and water flow conditions (Rieman and McIntyre 1993, p.

6). Juvenile and adult bull trout frequently inhabit side channels, stream margins, and pools with

suitable cover (Sexauer and James 1997, pp. 368-369).

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The size and age of bull trout at maturity depend upon life history strategy. Growth of resident

fish is generally slower than migratory fish; resident fish tend to be smaller at maturity and less

fecund (Goetz 1989, p. 15). Bull trout normally reach sexual maturity in 4 to 7 years and live as

long as 12 years. Bull trout are iteroparous (they spawn more than once in a lifetime), and both

repeat- and alternate-year spawning has been reported, although repeat-spawning frequency and

post-spawning mortality are not well documented (Leathe and Graham 1982, p. 95; Fraley and

Shepard 1989, p. 135; Pratt 1992, p. 8; Rieman and McIntyre 1996, p. 133).

Bull trout typically spawn from August to November during periods of decreasing water

temperatures. Migratory bull trout frequently begin spawning migrations as early as April, and

have been known to move upstream as far as 250 kilometers (km) (155 miles (mi)) to spawning

grounds (Fraley and Shepard 1989, p. 135). Depending on water temperature, incubation is

normally 100 to 145 days (Pratt 1992, p.1) and, after hatching, juveniles remain in the substrate.

Time from egg deposition to emergence may exceed 200 days. Fry normally emerge from early

April through May depending upon water temperatures and increasing stream flows (Pratt 1992,

p. 1).

The iteroparous reproductive system of bull trout has important repercussions for the

management of this species. Bull trout require two-way passage up and downstream, not only

for repeat spawning, but also for foraging. Most fish ladders, however, were designed

specifically for anadromous semelparous (fishes that spawn once and then die, and therefore

require only one-way passage upstream) salmonids. Therefore, even dams or other barriers with

fish passage facilities may be a factor in isolating bull trout populations if they do not provide a

downstream passage route.

Bull trout are opportunistic feeders with food habits primarily a function of size and life history

strategy. Resident and juvenile migratory bull trout prey on terrestrial and aquatic insects, macro

zooplankton and small fish (Boag 1987, p. 58; Goetz 1989, pp. 33-34; Donald and Alger 1993,

pp. 239-243). Adult migratory bull trout are primarily piscivores, known to feed on various fish

species (Fraley and Shepard 1989, p. 135; Donald and Alger 1993, p. 242).

A.4 Population Dynamics

The draft bull trout Recovery Plan (USDI 2002a, pp. 47-48) defined core areas as groups of

partially isolated local populations of bull trout with some degree of gene flow occurring

between them. Based on this definition, core areas can be considered metapopulations. A

metapopulation is an interacting network of local populations with varying frequencies of

migration and gene flow among them (Meefe and Carroll 1994, p. 188). In theory, bull trout

metapopulations (core areas) can be composed of two or more local populations, but Rieman and

Allendorf (2001, p. 763) suggest that for a bull trout metapopulation to function effectively, a

minimum 10 local populations are required. Bull trout core areas with fewer than five local

populations are at increased risk of local extirpation, core areas with between five and 10 local

populations are at intermediate risk, and core areas with more than 10 interconnected local

populations are at diminished risk (Fish and Wildlife Service 2002a, pp. 50-51).

14

The presence of a sufficient number of adult spawners is necessary to ensure persistence of bull

trout populations. In order to avoid inbreeding depression, it is estimated that a minimum of 100

spawners are required. Inbreeding can result in increased homozygosity of deleterious recessive

alleles which can in turn reduce individual fitness and population viability (Whitesel et al. 2004,

p. 36). For persistence in the longer term, adult spawning fish are required in sufficient numbers

to reduce the deleterious effects of genetic drift and maintain genetic variation. For bull trout,

Rieman and Allendorf (2001, p. 762) estimate that approximately 1,000 spawning adults within

any bull trout population are necessary for maintaining genetic variation indefinitely. Many

local bull trout populations individually do not support 1,000 spawners, but this threshold may be

met by the presence of smaller interconnected local populations within a core area.

For bull trout populations to remain viable (and recover), natural productivity should be

sufficient for the populations to replace themselves from generation to generation. A population

that consistently fails to replace itself is at an increased risk of extinction. Since estimates of

population size are rarely available, the productivity or population growth rate is usually

estimated from temporal trends in indices of abundance at a particular life stage. For example,

redd counts are often used as an indicator of a spawning adult population. The direction and

magnitude of a trend in an index can be used as a surrogate for growth rate.

Survival of bull trout populations is also dependent upon connectivity among local populations.

Although bull trout are widely distributed over a large geographic area, they exhibit a patchy

distribution even in pristine habitats (Rieman and McIntyre 1993, p. 7). Increased habitat

fragmentation reduces the amount of available habitat and increases isolation from other

populations of the same species (Saunders et al. 1991, p. 22). Burkey (1989, p. 76) concluded

that when species are isolated by fragmented habitats, low rates of population growth are typical

in local populations and their probability of extinction is directly related to the degree of

isolation and fragmentation. Without sufficient immigration, growth of local populations may be

low and probability of extinction high. Migrations also facilitate gene flow among local

populations because individuals from different local populations interbreed when some stray and

return to non natal streams. Local populations that are extirpated by catastrophic events may

also become reestablished in this manner.

In summary, based on the works of Rieman and McIntyre (1993, pp. 9-15) and Rieman and

Allendorf (2001, pp 756-763), the draft bull trout Recovery Plan identified four elements to

consider when assessing long-term viability (extinction risk) of bull trout populations: (1)

number of local populations, (2) adult abundance (defined as the number of spawning fish

present in a core area in a given year), (3) productivity, or the reproductive rate of the population,

and (4) connectivity (as represented by the migratory life history form).

A.5 Status and Distribution

As noted above, in recognition of available scientific information relating to their uniqueness and

significance, five population segments of the coterminous United States population of the bull

trout are considered essential to the survival and recovery of this species and are identified as:

(1) Jarbidge River, (2) Klamath River, (3) Coastal-Puget Sound, (4) St. Mary-Belly River, and

(5) Columbia River. Each of these segments is necessary to maintain the bull trout’s

15

distribution, as well as its genetic and phenotypic diversity, all of which are important to ensure

the species’ resilience to changing environmental conditions.

A summary of the current status and conservation needs of the bull trout within these units is

provided below. A comprehensive discussion of these topics is found in the draft bull trout

Recovery Plan (USDI 2002a, entire; 2005a, b; entire).

Central to the survival and recovery of the bull trout is the maintenance of viable core areas (Fish

and Wildlife Service 2002a, p. 54). A core area is defined as a geographic area occupied by one

or more local bull trout populations that overlap in their use of rearing, foraging, migratory, and

overwintering habitat, and in some cases their use of spawning habitat. Each of the population

segments listed below consists of one or more core areas. One hundred and twenty one core

areas are recognized across the United States range of the bull trout (USDI 2005, p. 9).

A core area assessment conducted by the Service for the 5 year bull trout status review

determined that of the 121 core areas comprising the coterminous listing, 43 are at high risk of

extirpation, 44 are at risk, 28 are at potential risk, 4 are at low risk and 2 are of unknown status

(USDI 2008, p. 29).

Jarbidge River: This population segment currently contains a single core area with six local

populations. Less than 500 resident and migratory adult bull trout, representing about 50 to 125

spawners, are estimated to occur within the core area. The current condition of the bull trout in

this segment is attributed to the effects of livestock grazing, roads, angler harvest, timber harvest,

and the introduction of non-native fishes (Fish and Wildlife Service 2004a, p. iii). The draft bull

trout Recovery Plan identifies the following conservation needs for this segment: (1) maintain

the current distribution of the bull trout within the core area, (2) maintain stable or increasing

trends in abundance of both resident and migratory bull trout in the core area, (3) restore and

maintain suitable habitat conditions for all life history stages and forms, and (4) conserve genetic

diversity and increase natural opportunities for genetic exchange between resident and migratory

forms of the bull trout. An estimated 270 to 1,000 spawning fish per year are needed to provide

for the persistence and viability of the core area and to support both resident and migratory adult

bull trout (Fish and Wildlife Service 2004a, p. 62-63). Currently this core area is at high risk of

extirpation (Fish and Wildlife Service 2005, p. 9).

Klamath River: This population segment currently contains 3 core areas and 12 local

populations. The current abundance, distribution, and range of the bull trout in the Klamath

River Basin are greatly reduced from historical levels due to habitat loss and degradation caused

by reduced water quality, timber harvest, livestock grazing, water diversions, roads, and the

introduction of non-native fishes. Bull trout populations in this unit face a high risk of

extirpation (Fish and Wildlife Service 2002b, p. iv). The draft bull trout Recovery Plan (Fish

and Wildlife Service 2002b, p. v) identifies the following conservation needs for this unit: (1)

maintain the current distribution of the bull trout and restore distribution in previously occupied

areas, (2) maintain stable or increasing trends in bull trout abundance, (3) restore and maintain

suitable habitat conditions for all life history stages and strategies, and (4) conserve genetic

diversity and provide the opportunity for genetic exchange among appropriate core area

populations. Eight to 15 new local populations and an increase in population size from about

16

3,250 adults currently to 8,250 adults are needed to provide for the persistence and viability of

the three core areas (Fish and Wildlife Service 2002b, p. vi).

Coastal-Puget Sound: Bull trout in the Coastal-Puget Sound population segment exhibit

anadromous, adfluvial, fluvial, and resident life history patterns. The anadromous life history

form is unique to this unit. This population segment currently contains 14 core areas and 67

local populations (Fish and Wildlife Service 2004b, p. iv; 2004c, pp. iii-iv). Bull trout are

distributed throughout most of the large rivers and associated tributary systems within this unit.

With limited exceptions, bull trout continue to be present in nearly all major watersheds where

they likely occurred historically within this unit. Generally, bull trout distribution has contracted

and abundance has declined, especially in the southeastern part of the unit. The current

condition of the bull trout in this population segment is attributed to the adverse effects of dams,

forest management practices (e.g., timber harvest and associated road building activities),

agricultural practices (e.g., diking, water control structures, draining of wetlands, channelization,

and the removal of riparian vegetation), livestock grazing, roads, mining, urbanization, angler

harvest, and the introduction of non-native species. The draft bull trout Recovery Plan (Fish and

Wildlife Service 2004b, pp. ix-x) identifies the following conservation needs for this unit: (1)

maintain or expand the current distribution of bull trout within existing core areas, (2) increase

bull trout abundance to about 16,500 adults across all core areas, and (3) maintain or increase

connectivity between local populations within each core area.

St. Mary-Belly River: This population segment currently contains six core areas and nine local

populations (Fish and Wildlife Service 2002c, p. v). Currently, bull trout are widely distributed

in the St. Mary River drainage and occur in nearly all of the waters that were inhabited

historically. Bull trout are found only in a 1.2-mile reach of the North Fork Belly River within

the United States. Redd count surveys of the North Fork Belly River documented an increase

from 27 redds in 1995 to 119 redds in 1999. This increase was attributed primarily to protection

from angler harvest (Fish and Wildlife Service 2002c, p. 37). The current condition of the bull

trout in this population segment is primarily attributed to the effects of dams, water diversions,

roads, mining, and the introduction of non-native fishes (Fish and Wildlife Service 2002c, p. vi).

The draft bull trout Recovery Plan (Fish and Wildlife Service 2002c, pp. v-ix) identifies the

following conservation needs for this unit: (1) maintain the current distribution of the bull trout

and restore distribution in previously occupied areas, (2) maintain stable or increasing trends in

bull trout abundance, (3) maintain and restore suitable habitat conditions for all life history

stages and forms, (4) conserve genetic diversity and provide the opportunity for genetic

exchange, and (5) establish good working relations with Canadian interests because local bull

trout populations in this unit are comprised mostly of migratory fish whose habitat is mainly in

Canada.

Columbia River: The Columbia River population segment includes bull trout residing in

portions of Oregon, Washington, Idaho, and Montana. Bull trout are estimated to have occupied

about 60 percent of the Columbia River Basin, and presently occur in 45 percent of the estimated

historical range (Quigley and Arbelbide 1997, p. 1177). This population segment currently

contains 97 core areas and 527 local populations. About 65 percent of these core areas and local

populations occur in Idaho and northwestern Montana.

17

The condition of the bull trout populations within these core areas varies from poor to good, but

generally all have been subject to the combined effects of habitat degradation, fragmentation and

alterations associated with one or more of the following activities: dewatering, road construction

and maintenance, mining and grazing, blockage of migratory corridors by dams or other

diversion structures, poor water quality, incidental angler harvest, entrainment into diversion

channels, and introduced non-native species.

The Service has determined that of the total 97 core areas in this population segment, 38 are at

high risk of extirpation, 35 are at risk, 20 are at potential risk, two are at low risk, and two are at

unknown risk (Fish and Wildlife Service 2005, pp. 1-94).

The draft bull trout Recovery Plan (USDI 2002a, p. v) identifies the following conservation

needs for this population segment: (1) maintain or expand the current distribution of the bull

trout within core areas, (2) maintain stable or increasing trends in bull trout abundance, (3)

maintain and restore suitable habitat conditions for all bull trout life history stages and strategies,

and (4) conserve genetic diversity and provide opportunities for genetic exchange.

Columbia River Recovery/Management Unit: Achieving recovery goals within each

management unit is critical to recovering the Columbia River population segment. Recovering

bull trout in each management unit would maintain the overall distribution of bull trout in their

native range. Individual core areas are the foundation of management units and conserving core

areas and their habitats within management units preserves the genotypic and phenotypic

diversity that will allow bull trout access to diverse habitats and reduce the risk of extinction

from stochastic events. The continued survival and recovery of each individual core area is

critical to the persistence of management units and their role in the recovery of a population

segment (USDI 2002a, p. 54).

The draft bull trout Recovery Plan (USDI 2002a, p. 2) identified 22 recovery units within the

Columbia River population segment. These units are now referred to as management units.

Management units are groupings of bull trout with historical or current gene flow within them

and were designated to place the scope of bull trout recovery on smaller spatial scales than the

larger population segments. The action area is encompassed by the Clark Fork management unit.

Clark Fork River Management Unit: The Clark Fork Management Unit and Clark Fork River

Basin CHU are the same geographical scale. This CHU is essential to maintaining bull trout

distribution within this unique geographic region of the draft Columbia Headwaters Recovery

Unit in large part because it represents the evolutionary heart of the migratory adfluvial bull trout

life history form.

In the Clark Fork River Management Unit, which includes all of the Clark Fork River Basin

from Albeni Falls Dam (outlet of Lake Pend Oreille) upstream to Montana headwaters, the

Service described 35 core areas for bull trout. At least 152 local populations of bull trout have

been identified associated within these core areas (USDI 2002b). The Clark Fork River

Management Unit is among the largest and most diverse across the species range and contains

the highest number of core areas of any management unit, due in large part to the preponderance

of isolated headwater lakes in the system. Bull trout within the larger and more diverse core

18

areas are typically characterized by having relatively small amounts of genetic diversity within a

local population but high levels of divergence between them (see for example Spruell et al. 1999,

Kanda and Allendorf 2001, Neraas and Spruell 2001).

The risk assessment or ranking portion of the bull trout status review (USDI 2005b) was

modeled to assess the relative status of each of the 118 core areas. The model used to rank the

relative risk to bull trout was based on the Natural Heritage Program’s NatureServe Conservation

Status Assessment Criteria, which had been applied in previous assessments of fish status,

including bull trout (Master et al. 2003, MNHP 2004). The model integrated four factors:

population abundance, distribution, population trend, and threats (referred to as a C Rank in the

model). See USDI (2005b) for a complete description of the ranking process.

Results of the status review (USDI 2005b) indicated that Clark Fork Management Unit has 18

core areas rated at high risk, 5 rated as at risk and 7 at potential risk. A core area rated at high

risk was functioning “at risk” because of very limited and/or declining numbers, range, and/or

habitat, making the bull trout in this core area vulnerable to extirpation (USDI 2005b).

The Service considers many of the core areas in the Clark Fork River drainage to be at risk of

extirpation due in part to natural isolation, single life-history form, and low abundance.

Expansion of nonnative species is the single largest human-caused threat in most of the core

areas. Dams and degraded habitat have also contributed to bull trout declines across this

Management Unit. The status of the Lower Clark Fork core area is described in the effects

section of this biological opinion.

A.6 Global Climate Change

Global climate change, and the related warming of global climate, have been well documented

(IPCC 2007, ISAB 2007, WWF 2003). Evidence of global climate change/warming includes

widespread increases in average air and ocean temperatures and accelerated melting of glaciers,

and rising sea level. Given the increasing certainty that climate change is occurring and is

accelerating (IPCC 2007, Battin et al. 2007), we can no longer assume that climate conditions in

the future will resemble those in the past.

Patterns consistent with changes in climate have already been observed in the range of many

species and in a wide range of environmental trends (ISAB 2007, Hari et al. 2006, Rieman et al.

2007). Climate change has the potential to profoundly alter the aquatic ecosystems upon which

the bull trout depends via alterations in water yield, peak flows, and water temperatures in

streams and large waterbodies, and an increase in the frequency and magnitude of catastrophic

wildfires in adjacent terrestrial habitats (Bisson et al. 2003). In the Pacific Northwest, most

climate change predictive models project warmer air temperatures, increases in winter

precipitation, and decreases in summer precipitation. Warmer temperatures will lead to more

precipitation falling as rain rather than snow. As the seasonal amount of snow pack diminishes,

the timing and volume of stream flow are likely to change and peak river flows are likely to

increase in affected areas. Higher air temperatures are also likely to increase water temperatures

(ISAB 2007).

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All life stages of the bull trout rely on cold water. Increasing air temperatures are likely to

impact the availability of suitable cold water habitat. For example, ground water temperature is

generally correlated with mean annual air temperature, and has been shown to strongly influence

the distribution of other chars. Ground water temperature is linked to bull trout selection of

spawning sites, and has been shown to influence the survival of embryos and early juvenile

rearing of bull trout (Rieman et al. 2007). Increases in air temperature are likely to be reflected

in increases in both surface and groundwater temperatures. Climate change is likely to affect

both the frequency and magnitude of fires, especially in warmer, drier areas such as are found in

the Flathead and Swan Lake core areas.

There is still a great deal of uncertainty associated with predictions relative to the timing,

location, and magnitude of future climate change. It is also likely that the intensity of effects

will vary by region and some populations of bull trout appear to face higher risk than others

(ISAB 2007; Rieman et al. 2007). There is little doubt that climate change is and will be an

important factor affecting bull trout distribution. As its distribution contracts, patch size

decreases and connectivity is truncated, bull trout populations that may be currently connected

may face increasing isolation, which could accelerate the rate of local extirpation beyond that

resulting from changes in stream temperature alone (Rieman et al. 2007).

B. Critical Habitat

B.1 Legal Status

Ongoing litigation resulted in the U.S. District Court for the District of Oregon granting the

Service a voluntary remand of the 2005 critical habitat designation. Subsequently the Service

published a proposed critical habitat rule on January 14, 2010 (75 FR 2260) and a final rule on

October 18, 2010 (75 FR 63898). The rule became effective on November 17, 2010. A

justification document was also developed to support the rule and is available on our website

(http://www.fws.gov/pacific/bulltrout). The scope of the designation involved the species’

coterminous range, which includes the Jarbidge River, Klamath River, Coastal-Puget Sound, St.

Mary-Belly River, and Columbia River population segments (also considered as interim recovery

units)1.

Rangewide, the Service designated reservoirs/lakes and stream/shoreline miles in 32 critical

habitat units (CHU) as bull trout critical habitat (Table 3). Designated bull trout critical habitat

is of two primary use types: (1) spawning and rearing; and (2) foraging, migrating, and

overwintering (FMO).

The final rule increased the amount of designated bull trout critical habitat by approximately 76

percent for miles of stream/shoreline and by approximately 71 percent for acres of lakes and

reservoirs compared to the 2005 designation.

1 The Service’s 5 year review (Fish and Wildlife Service 2008, pg. 9) identifies six draft recovery units. Until the

bull trout draft recovery plan is finalized, the current five interim recovery units are in affect for purposes of section

7 jeopardy analysis and recovery. The adverse modification analysis does not rely on recovery units.

20

This rule also identifies and designates as critical habitat approximately 1,324km (823 miles) of

streams/shorelines and 6,759 ha (16,701 acres) of lakes/reservoirs of unoccupied habitat to

address bull trout conservation needs in specific geographic areas in several areas not occupied at

the time of listing. No unoccupied habitat was included in the 2005 designation. These

unoccupied areas were determined by the Service to be essential for restoring functioning

migratory bull trout populations based on currently available scientific information. These

unoccupied areas often include lower mainstem river environments that can provide seasonally

important migration habitat for bull trout. This type of habitat is essential in areas where bull

trout habitat and population loss over time necessitates reestablishing bull trout in currently

unoccupied habitat areas to achieve recovery.

Table 3. Stream/shoreline distance and reservoir/lake area designated as bull trout critical habitat

by state (final rule October 18, 2010).

State Stream/Shoreline

Miles

Stream/Shoreline

Kilometers

Reservoir

/Lake

Acres

Reservoir/

Lake

Hectares

Idaho 8,772 14,117 170,218 68,885

Montana 3,057 4,919 221,471 89,626

Nevada 72 116 - -

Oregon 2,836 4,564 30,256 12,244

Oregon/Idaho 108 173 - -

Washington 3,793 6,105 66,308 26,834

Washington (marine) 754 1,213 - -

Washington/Idaho 37 60 - -

Washington/Oregon 301 485 - -

Total 19,730 31,752 488,253 197,589

The final rule continues to exclude some critical habitat segments based on a careful balancing of

the benefits of inclusion versus the benefits of exclusion. Critical habitat does not include: (1)

waters adjacent to non-Federal lands covered by legally operative incidental take permits for

habitat conservation plans (HCPs) issued under section 10(a)(1)(B) of the Endangered Species

Act of 1973, as amended (Act), in which bull trout is a covered species on or before the

publication of this final rule; (2) waters within or adjacent to Tribal lands subject to certain

commitments to conserve bull trout or a conservation program that provides aquatic resource

protection and restoration through collaborative efforts, and where the Tribes indicated that

inclusion would impair their relationship with the Service; or (3) waters where impacts to

national security have been identified (75 FR 63898). Excluded areas are approximately 10

percent of the stream/shoreline miles and 4 percent of the lakes and reservoir acreage of

designated critical habitat. Each excluded area is identified in the relevant CHU text, as

identified in paragraphs (e)(8) through (e)(41) of the final rule. It is important to note that the

exclusion of waterbodies from designated critical habitat does not negate or diminish their

importance for bull trout conservation. Because exclusions reflect the often complex pattern of

land ownership, designated critical habitat is often fragmented and interspersed with excluded

stream segments.

Conservation Role and Description of Critical Habitat: The conservation role of bull trout

critical habitat is to support viable core area populations (75 FR 63943). The core areas reflect

21

the metapopulation structure of bull trout and are the closest approximation of a biologically

functioning unit for the purposes of recovery planning and risk analyses. CHUs generally

encompass one or more core areas and may include FMO areas, outside of core areas, that are

important to the survival and recovery of bull trout.

As previously noted, 32 CHUs within the geographical area occupied by the species at the time

of listing are designated under the final rule. Twenty-nine of the CHUs contain all of the

physical or biological features identified in this final rule and support multiple life-history

requirements. Three of the mainstem river units in the Columbia and Snake River basins contain

most of the physical or biological features necessary to support the bull trout’s particular use of

that habitat, other than those physical and biological features associated with Primary

Constituent Elements (PCEs) 5 and 6, which relate to breeding habitat (see list below).

The primary function of individual CHUs is to maintain and support core areas, which (1)

contain bull trout populations with the demographic characteristics needed to ensure their

persistence and contain the habitat needed to sustain those characteristics (Rieman and McIntyre

1993, p. 19); (2) provide for persistence of strong local populations, in part, by providing habitat

conditions that encourage movement of migratory fish (MBTSG 1998, pp. 48-49; Rieman and

McIntyre 1993, pp. 22-23); (3) are large enough to incorporate genetic and phenotypic diversity,

but small enough to ensure connectivity between populations (MBTSG 1998, pp. 48-49; Rieman

and McIntyre 1993, pp. 22-23); and (4) are distributed throughout the historic range of the

species to preserve both genetic and phenotypic adaptations (MBTSG 1998, pp. 13-16; Rieman

and Allendorf 2001, p. 763; Rieman and McIntyre 1993, p. 23).

The Olympic Peninsula and Puget Sound CHUs are essential to the conservation of

amphidromous bull trout, which are unique to the Coastal-Puget Sound population segment.

These CHUs contain marine nearshore and freshwater habitats, outside of core areas, that are

used by bull trout from one or more core areas. These habitats, outside of core areas, contain

PCEs that are critical to adult and subadult foraging, migrating, and overwintering.

In determining which areas to propose as critical habitat, the Service considered the physical and

biological features that are essential to the conservation of bull trout and that may require special

management considerations or protection. These features are the PCEs laid out in the

appropriate quantity and spatial arrangement for conservation of the species. The PCEs for bull

trout are those habitats components that are essential for the primary biological needs of

foraging, reproducing, rearing of young, dispersal, genetic exchange, or sheltering (75 FR 63898,

p. 2306). The PCEs of designated critical habitat are:

1. Springs, seeps, groundwater sources, and subsurface water connectivity (hyporheic flows)

to contribute to water quality and quantity and provide thermal refugia.

2. Migration habitats with minimal physical, biological, or water quality impediments

between spawning, rearing, overwintering, and freshwater and marine foraging habitats,

including, but not limited to, permanent, partial, intermittent, or seasonal barriers.

22

3. An abundant food base, including terrestrial organisms of riparian origin, aquatic

macroinvertebrates, and forage fish.

4. Complex river, stream, lake, reservoir, and marine shoreline aquatic environments and

processes that establish and maintain these aquatic environments, with features such as

large wood, side channels, pools, undercut banks and unembedded substrates, to provide a

variety of depths, gradients, velocities, and structure.

5. Water temperatures ranging from 2 to 15 C (36 to 59 F), with adequate thermal refugia

available for temperatures that exceed the upper end of this range. Specific temperatures

within this range will depend on bull trout life-history stage and form; geography;

elevation; diurnal and seasonal variation; shading, such as that provided by riparian

habitat; streamflow; and local groundwater influence.

6. In spawning and rearing areas, substrate of sufficient amount, size, and composition to

ensure success of egg and embryo overwinter survival, fry emergence, and young-of-the-

year and juvenile survival. A minimal amount of fine sediment, generally ranging in size

from silt to coarse sand, embedded in larger substrates, is characteristic of these

conditions. The size and amounts of fine sediment suitable to bull trout will likely vary

from system to system.

7. A natural hydrograph, including peak, high, low, and base flows within historic and

seasonal ranges or, if flows are controlled, minimal flow departures from a natural

hydrograph.

8. Sufficient water quality and quantity such that normal reproduction, growth, and survival

are not inhibited.

9. Sufficiently low levels of occurrence of nonnative predatory (e.g., lake trout, walleye,

northern pike, smallmouth bass); interbreeding (e.g., brook trout); or competing (e.g.,

brown trout) species that, if present, are adequately temporally and spatially isolated from

bull trout.

B.2 Current Range-wide Condition of Bull Trout Critical Habitat

The condition of designated bull trout critical habitat varies across its range from poor to good.

Although still relatively widely distributed across its historic range, the bull trout occurs in low

numbers in many areas, and populations are considered depressed or declining across much of its

range (67 FR 71240). This condition reflects the condition of bull trout habitat. The primary

land and water management activities impacting the physical and biological features essential to

the conservation of bull trout include timber harvest and road building, agriculture and

agricultural diversions, livestock grazing, dams, mining, urbanization and residential

development, and non-native species presence or introduction (75 FR 2282). There is

widespread agreement in the scientific literature that many factors related to human activities

have impacted bull trout and their habitat, and continue to do so. Among the many factors that

23

contribute to degraded PCEs, those which appear to be particularly significant and have resulted

in a legacy of degraded habitat conditions are as follows:

1. Fragmentation and isolation of local populations due to the proliferation of dams and

water diversions that have eliminated habitat, altered water flow and temperature regimes,

and impeded migratory movements (Dunham and Rieman 1999, p. 652; Rieman and

McIntyre 1993, p. 7).

2. Degradation of spawning and rearing habitat and upper watershed areas, particularly

alterations in sedimentation rates and water temperature, resulting from forest and

rangeland practices and intensive development of roads (Fraley and Shepard 1989, p. 141;

MBTSG 1998, pp. ii - v, 20-45).

3. The introduction and spread of nonnative fish species, particularly brook trout and lake

trout, as a result of fish stocking and degraded habitat conditions, which compete with bull

trout for limited resources and, in the case of brook trout, hybridize with bull trout (Leary

et al. 1993, p. 857; Rieman et al. 2006, pp. 73-76).

4. In the Coastal-Puget Sound region where amphidromous bull trout occur, degradation of

mainstem river FMO habitat, and the degradation and loss of marine nearshore foraging

and migration habitat due to urban and residential development.

5. Degradation of FMO habitat resulting from reduced prey base, roads, agriculture,

development, and dams.

One objective of the final rule was to identify and protect those habitats that provide resiliency

for bull trout use in the face of climate change. Over a period of decades, climate change may

directly threaten the integrity of the essential physical or biological features described in PCEs 1,

2, 3, 5, 7, 8, and 9. Protecting bull trout strongholds and cold water refugia from disturbance

and ensuring connectivity among populations were important considerations in addressing this

potential impact. Additionally, climate change may exacerbate habitat degradation impacts both

physically (e.g., decreased base flows, increased water temperatures) and biologically (e.g.,

increased competition with non-native fishes).

B.3 Status of the Clark Fork River Critical Habitat Unit (CHU) 31

The Clark Fork River Basin CHU includes 5,356.0 km (3,328.1 mi) of streams and 119,620.1 ha

(295,586.6 ac) of lakes and reservoirs designated as critical habitat. The sub-units within this

unit provide spawning, rearing, foraging, migratory, connecting, and overwintering habitat. For

a detailed description of this unit and sub-units, for justification of why this CHU, included

CHSUs, or in some cases individual water bodies are designated as critical habitat, and for

documentation of occupancy by bull trout, see Service (2010), or

http://www.fws.gov/pacific/bulltrout.

The Clark Fork River Basin CHU is essential to maintaining bull trout distribution within

24

this unique geographic region of the Columbia Headwaters Recovery Unit in large part because

it represents the evolutionary heart of the migratory adfluvial bull trout life history form (USDI

2009a, p. 32). Flathead Lake and Lake Pend Oreille are the two largest lakes in the range of the

species, and bull trout from those core areas historically grew to be large and migrated upstream

up to 322 km (200 miles) to spawning and rearing habitats. These habitats were partially

fragmented by hydroelectric dams and other manmade barriers but are increasingly being

reconnected with dam removal (Milltown Dam) and improved fish passage (Cabinet Gorge,

Noxon Rapids, Thompson Falls). The resident life history form of bull trout is minimally

present in this CHU and fluvial bull trout play a reduced role relative to adfluvials. The two

major lakes (Flathead and Pend Oreille), as well as over 20 additional core areas established in

smaller headwater lakes that are isolated from Flathead and Pend Oreille to varying degrees, are

the primary refugia for the naturally occurring adfluvial form of bull trout across their range.

The action area for this biological opinion includes a portion of the Lower Clark Fork core area

that extends 600 feet up and 1300 feet downstream of the project site, encompassing

approximately 0.36 river miles. The Lower Clark Fork CHSU is essential to bull trout

conservation because it provides an important portion of the spawning and rearing habitat for

Lake Pend Oreille, as well as an essential migratory corridor for bull trout from Lake Pend

Oreille to be able to access productive watersheds upstream of this CHSU.

C. Analysis of Species/Critical Habitat Likely to be Affected

The proposed action will occur in the Lower Clark Fork core area and Lower Clark Fork CHSU.

The Lower Clark Fork core area is one of 25 primary core areas in the Clark Fork Management

Unit. In this Management Unit, a distinction has been made between two types of core areas

(primary and secondary core areas) based mostly on the size, connectedness, and complexity of

the associated watershed and the degree of natural population isolation (USDI 2002, p.13). In

2010, the Service identified the Lower Clark Fork CHSU as essential to bull trout conservation

because it provides an important portion of the spawning and rearing habitat for Lake Pend

Oreille, as well as an essential migratory corridor for bull trout from Lake Pend Oreille to be able

to access productive watersheds upstream of this CHSU. This CHSU contains approximately

107 miles of spawning and rearing (SR) habitat, 189 miles of stream/riverine foraging,

migratory, and overwintering (FMO) habitat, and 9,719 acres of FMO habitat in lakes and

reservoirs that are designated as critical habitat. These designated segments provide the

necessary habitat (SR and FMO) that support the local populations in the Lower Clark Fork core

area needed for recovery.

C.1 Previous Consultations and Conservation Efforts

Consulted-on effects are those effects that have been analyzed through section 7 consultation as

reported in a biological opinion. These effects are an important component of objectively

characterizing the current condition of the species. To assess consulted-on effects to bull trout,

we analyzed all of the biological opinions received by the Region 1 and Region 6 Service

Offices, from the time of listing until August 2003; this summed to 137 biological opinions. Of

these, 124 biological opinions (91 percent) applied to activities affecting bull trout in the

Columbia Basin population segment, 12 biological opinions (9 percent) applied to activities

25

affecting bull trout in the Coastal-Puget Sound population segment, 7 biological opinions (5

percent) applied to activities affecting bull trout in the Klamath Basin population segment, and

one biological opinion (< 1 percent) applied to activities affecting the Jarbidge and St. Mary-

Belly population segments (Note: these percentages do not add to 100, because several

biological opinions applied to more than one population segment). The geographic scale of these

consultations varied from individual actions (e.g., construction of a bridge or pipeline) within

one basin to multiple-project actions occurring across several basins.

A total of 110 biological opinions or other forms of issued take (i.e., Section 10 permits) were

issued for the Clark Fork River MU since listing to February 3, 2014 (39 from listing to August

2003 and 71 from August 2003 to now). Of these, 15 biological opinions have been issued for

the Lower Clark Fork River core area. All of the opinions have included mandatory terms and

conditions, which are binding on the action agency, in order to reduce the potential impacts of

anticipated incidental, take to bull trout.

C.2 Conservation Needs

The recovery planning process for the bull trout (Fish and Wildlife Service 2002a, p. 49) has

identified the following conservation needs (goals) for bull trout recovery: (1) maintain the

current distribution of bull trout within core areas as described in recovery unit chapters, (2)

maintain stable or increasing trends in abundance of bull trout as defined for individual recovery

units, (3) restore and maintain suitable habitat conditions for all bull trout life history stages and

strategies, and (4) conserve genetic diversity and provide opportunity for genetic exchange.

The draft bull trout Recovery Plan (Fish and Wildlife Service 2002a, p. 62) identifies the

following tasks needed for achieving recovery: (1) protect, restore, and maintain suitable habitat

conditions for bull trout, (2) prevent and reduce negative effects of non-native fishes, such as

brook trout, and other non-native taxa on bull trout, (3) establish fisheries management goals and

objectives compatible with bull trout recovery, (4) characterize, conserve, and monitor genetic

diversity and gene flow among local populations of bull trout, (5) conduct research and

monitoring to implement and evaluate bull trout recovery activities, consistent with an adaptive

management approach using feedback from implemented, site-specific recovery tasks, (6) use all

available conservation programs and regulations to protect and conserve bull trout and bull trout

habitats, (7) assess the implementation of bull trout recovery by management units, and (8)

revise management unit plans based on evaluations.

Another threat now facing bull trout is warming temperature regimes associated with global

climate change. Because air temperature affects water temperature, species at the southern

margin of their range that are associated with cold water patches, such as bull trout, may become

restricted to smaller, more disjunct patches or become extirpated as the climate warms (Rieman

et al. 2007, p. 1560). Rieman et al. (2007, pp. 1558, 1562) concluded that climate is a primary

determining factor in bull trout distribution. Some populations already at high risk, such as the

Jarbidge, may require “aggressive measures in habitat conservation or restoration” to persist

(Rieman et al. 2007, p. 1560). Conservation and restoration measures that would benefit bull

trout include protecting high quality habitat, reconnecting watersheds, restoring flood plains, and

26

increasing site-specific habitat features important for bull trout, such as deep pools or large

woody debris (Kinsella 2005, entire).

V. Environmental Baseline

Regulations implementing the Act, as amended (16 U.S.C. 1531 et seq.; 50 CFR 402.02) define

the environmental baseline as the past and present impacts of all federal, state, or private actions

and other human activities in the action area. Also included in the environmental baseline are

the anticipated impacts of all proposed federal projects in the action area that have already

undergone section 7 consultation, and the impacts of state and private actions in the action area

that are contemporaneous with the consultation in progress. The environmental baseline should

characterize the effects of past and ongoing human factors leading to the current status of the

species, their habitats, and ecosystem within the action area. The action area for this biological

opinion includes the portion of the Lower Clark Fork core area and CHSU that encompasses the

Thompson River—Goat Creek (6th

code watershed #170102130407) sub-watershed.

Baseline conditions for bull trout were assessed using information in the Bull Trout Core Area

Templates (USDI 2005a), Consistency Check with the 5-year Bull Trout Review, Lolo National

Forest (USDA 2007) draft recovery plan (USDI 2002a; USDI 2002b), Final Rule for Bull Trout

Critical Habitat, and other sources of information.

A. Status of the Species and Critical Habitat within the Action Area

Lower Clark Fork Core Area: Bull trout populations in the Lower Clark Fork River core area

were first exposed to significant anthropogenic impacts with the construction of the Thompson

Falls Dam in 1913. This dam blocked upstream migration of bull trout from Lake Pend Oreille,

and effectively cut off all upstream spawning habitat, affecting bull trout populations in core

areas upstream from the Lower Clark Fork River. Within the Lake Pend Oreille core area,

Thompson Falls Dam cut off the Thompson River from the rest of the core area. In 1952 and

1958, respectively, Cabinet Gorge and Noxon Dams were constructed. These dams also blocked

access, resulting in only a few smaller tributaries remaining to support the entire Lake Pend

Oreille population. With the completion of the three dams, the bull trout population was

fragmented into four populations: Lake Pend Oreille, Cabinet Gorge and tributaries, Noxon and

tributaries, and above Thompson Falls Dam. Consequently, only downstream connectivity

remained (USDA 2013).

Other smaller scale impacts to bull trout occurred throughout the core area, including grazing

and agricultural development along many important low gradient spawning streams, road and

energy corridor development, and logging and road development in tributary streams. From the

1930’s through the 1960’s, bull trout populations in the Lower Clark Fork River core area

continued to decline due to increasing land utilization that impacted stream habitats. The

Thompson River was heavily impacted by two logging roads that paralleled the stream. Many of

the wide riparian valleys in key spawning tributaries like Prospect Creek, Vermillion River, and

Thompson River were impacted by grazing and logging. Much of the impact from logging came

in the 1970’s and 1980’s due to a rapid expansion of road construction and logging in the

tributaries, and resulted in extensive fragmentation of bull trout populations at undersized culvert

27

crossings (USDA 2013). Currently, the greatest threats to bull trout in this core area consist of

fish passage issues associated with dams, non-native species, and forest management practices

and forest roads (USDI 2008).

Comprehensive redd counts in three of the four portions of the Lower Clark Fork River core area

(lower Flathead River excepted) have been conducted in recent years in association with the

Avista Native Salmonid Restoration Program. Between 2001 and 2008, redd counts have been

conducted in full or partial index reaches of the mainstem, East Fork and South Fork Bull River,

Rock Creek, Swamp Creek, Vermilion River, Graves Creek, Prospect Creek, Fishtrap Creek and

West Fork Fishtrap, Beatrice Creek, and West Fork Thompson River (USDI 2008). Collectively,

these redd counts have been estimated to include greater than 80% of the total bull trout

spawning that occurs in the system (with exception of the lower Flathead). These results indicate

that the total adult bull trout population for these portions of the core area is at least stable, with

the strongest year on record occurring in 2006 (145 redds). Based on a standard expansion factor

of 3.2 adults per redd, the 2006 data would indicate at minimum an adult population approaching

500 fish (USDI 2008).

During the relicensing process for Avista dams, programs have been developed to trap and

transport bull trout around the three dams in an effort to more fully understand spawning

movements and future recovery efforts. Additionally, a fish ladder has been installed by PPL in

the Thompson Falls Dam, and future work on the other two dams to allow for unmitigated fish

passage is occurring. Prior to the construction of the fish ladder at Thompson Falls Dam, the

dam prevented upstream migration to known bull trout tributaries in the Thompson River, the

lower Flathead River (Jocko River and Mission Creek drainages) downstream of Kerr Dam, and

the middle Clark Fork River drainage. Genetic data analyzed (since 2004) from adult bull trout

collected at the base of Cabinet Gorge Dam in the lower Clark Fork River drainage have verified

that the specific natal tributaries for some of the returning bull trout are upstream of Thompson

Falls Dam (GEI Consultants 2013, p. 31).

Through the trap and transport program at the dams between 2001 and 2011, Avista has learned

through genetic testing that 20% of the 611 individual bull trout captured downstream of the

Cabinet Gorge Dam originated from tributaries upstream of the Thompson Falls Dam. Of those

20%, 75 fish (61% of the 20%) originated from the Thompson River drainage (GEI Consultants

2013, p. 31). These data indicate downstream bull trout movements are not limited to the lower

Clark Fork River, and that the adfluvial life history of bull trout still exists in the Lower Clark

Fork River core area (GEI Consultants 2013, p. 31).

Within the project area, the confluence of the Thompson River with the Clark Fork River is

located approximately 6.3 river miles upstream of the Thompson Falls Dam. The lower section

of the Thompson River, which includes the area from the 17-mile bridge to the mouth of the

river, is higher in gradient, flowing through a confined canyon and the project area. The lower

half of the drainage is generally a narrower valley with a greater frequency of bedrock outcrops

and sections of high gradient channel, steep valley walls, and a few short gorge sections (GEI

Consultants 2013, p. 13). Within the Thompson River drainage, the warmest water temperatures

in the Thompson River occur just downstream from the confluence of the Little Thompson River

and above the confluence of Fishtrap Creek. In most rivers and streams the warmest water

28

temperatures occur near their mouths, but in the Thompson River, the coolest water temperatures

occur near its mouth. Fish species distribution in the Thompson River varies as a result of the

temperature gradient in the drainage. The lower, cooler portion of the river contains primarily a

rainbow trout (Oncorhynchus mykiss) fishery, which is most popular with anglers, and the area

between the mouth of the Thompson River and the confluence of Fishtrap Creek serves as a

migratory corridor for bull trout (GEI Consultants 2013, p. 15). Within the Thompson River

drainage, the West Fork Thompson River and Fishtrap Creek contain the primary spawning and

rearing habitats.

Additional information and a comprehensive review of the status of bull trout core areas in the

Clark Fork can be found in the Service’s Bull Trout Core Area Templates Complete Core Area

by Core Area Analysis (USDI 2008).

B. Factors Affecting Species Environment (Habitat) Within the Action Area

Within the Lower Clark Fork River CHSU, threats to bull trout and bull trout critical habitat

consist of fish passage issues due to the dams, non-native species, and forest management

practices and forest roads (USDI 2008). Also at issue is water quality impairment due to

temperature. Major fish passage barriers in the Lower Clark Fork River CHSU (Cabinet Gorge

Dam, Noxon Rapids Dam, Thompson Falls Dam, Milltown Dam) are being gradually reduced or

eliminated (Milltown removed 2008; Thompson Falls fish passage 2010). For those still in

operation (Cabinet Gorge and Noxon) trap and transport strategies are being used to reduce the

impacts. As a result, fragmentation is being reduced and connectivity restored, diminishing the

highest ranking threat. A fish ladder was installed on Thompson Falls dam in 2010 and has been

operational since the spring of 2011, which should help fluvial populations reach the Thompson

River. However, it is not expected that these operations will fully resolve the problem of

fragmentation in the Clark Fork River system (USDA 2013).

Non-native species (brook trout, brown trout, lake trout, northern pike, walleye, etc.) are

increasingly impacting efforts to recover bull trout and habitat in the reservoirs favors many of

those populations over native species (USDI 2008). Extensive information is being collected on

the overlap with and potential superimposition of brown trout redds in important bull trout

drainages (Moran 2004). Studies are ongoing related to concerns that northern pike negatively

interact with bull trout and predate on juvenile bull trout in Cabinet Gorge Reservoir (Bernall

and Moran 2004). There are also concerns about negative interactions with high densities of

brook trout in many watersheds and the potential for an increasing population of recently

illegally introduced walleye that are reproducing in Noxon Reservoir. To date, control actions

on these species have not been initiated, pending further analysis. Thus, the combined impact of

dams on the Clark Fork River is expected to remain the highest ranking threat into the future

(USDI 2008).

Within the project area, there is a dual road system along the Thompson River was constructed in

the 1950’s. County Road 56 and Forest Road 9991 run the entire length of the Thompson River

from Highway 200 to US Highway 2 near the Thompson Chain of Lakes. These two roads

closely parallel the river on each side for the first 18 miles, then alternate to the other side by

crossing the Thompson River and periodically paralleling or crossing the stream in the upper 20

29

miles. The most significant effects are seen for the first 18 miles. The dual road system has

caused the river to be confined, which, in turn, has led to habitat that is oversimplified. There is a

general lack of large woody debris and subsequently large, high quality pools. The dual road

system also contributes large amounts of sediment to the river. The loss of overhead cover from

the dual road system also leads to increased stream temperatures. The dual road system has also

indirectly caused an increase in fishing because both side of the river are easily accessible by

vehicle (USDA 2013).

As previously mentioned, within the Thompson River drainage, the warmest water temperatures

in the Thompson River occur just downstream from the confluence of the Little Thompson River

and above the confluence of Fishtrap Creek. In most rivers and streams the warmest water

temperatures occur near their mouths, but in the Thompson River, the coolest water temperatures

occur near its mouth. Water temperature downstream of the confluence of Fishtrap Creek and

Thompson River, which is located between River Mile (RM) 15 and 16, is much cooler than

water temperature upstream at Fishtrap Creek. In 2004, the mean weekly maximum temperature

(MWMT) in the Thompson River at RM 16 (upstream of Fishtrap Creek) was 72.5oF, while the

MWMT at RM 15 (downstream of Fishtrap Creek) was 61.5 oF (GEI Consultants 2013). The

Thompson River has a series of lakes in the headwaters. The large surface area of the lakes

results in warm water temperatures. However, none of the tributaries of the upstream portions of

the Thompson River have a large enough cold water volume to cool the mainstem Thompson

River to a sufficient extent to bring the MWMT into the suitable or marginal range for bull trout

(GEI Consultants 2013, p. 41).

VI. Effects of the Action

"Effects of the action" refer to the direct and indirect effects of an action on the species or critical

habitat, which, when combined with the effects of other activities interrelated or interdependent

with that action, will be added to the environmental baseline. Direct effects are considered

immediate effects of the project on the species or its habitat. Indirect effects are those caused by

the action and are later in time, but are still reasonably certain to occur. Interrelated actions are

part of a larger action and depend upon the larger action for their justification. Interdependent

actions have no independent utility apart from the action under consultation.

A. Analyses for Effects of the Action

This biological opinion evaluates the impacts of replacing the existing 5-span, 428 feet long

Thompson River bridge with a 3-span, 438 feet long welded girder bridge on bull trout and bull

trout critical habitat. The primary factor by which bull trout and bull trout critical habitat have

the potential to be adversely affected by the action is through the potential for a temporary

barrier, should portions of the existing bridge drop into the existing channel during demolition.

In order to minimize the likelihood of this occurring, the Administration and Department will

implement the 9 coordination and conservation measures listed in this document (pp. 15-16).

To define the habitat conditions for the species and its critical habitat and assess impacts from

proposed actions, the Service uses the “A Framework to Assist in Making Endangered Species

Act Determinations of Effect for Individual or Grouped Actions at the Bull Trout Subpopulation

30

Watershed Scale” (framework/matrix; USDI, 1998b). The framework/matrix defines the

biological requirements for bull trout and facilitates the evaluation and relevance of the

environmental baseline to the current status of the species to determine the effect of the action

and whether the species can be expected to survive with an adequate potential for recovery. The

evaluation of the population and habitat indicators were conducted at the 5th

or 6th

field

Hydrologic Unit Code (HUC or sub-watersheds) scales to establish the environmental baseline.

Definitions for the baseline determinations Functioning Appropriately (FA), Functioning at Risk

(FAR), and Functioning at Unacceptable Risk (FUR) for each of the habitat indicators are

discussed in USDI 1998a, Table 1 at page 20. Analysis of the habitat indicators can provide a

thorough evaluation of the existing baseline condition and potential project impacts to the PCEs.

Appendix A explains the relationship between the PCEs for bull trout critical habitat and the

framework habitat indicators.

Habitat indicators in a sub-watershed that are FA provide habitats that maintain strong and

significant populations, are interconnected and promote recovery of a proposed or listed species

or its critical habitat to a status that will provide self-sustaining and self-regulating populations.

When a habitat indicator is FAR, they provide habitats for persistence of the species but in more

isolated populations and may not promote recovery of a proposed or listed species or its habitat

without active or passive restoration efforts. FUR suggests the proposed or listed species

continues to be absent from historical habitat, or is rare or being maintained at a low population

level; although the habitat may maintain the species at this low persistence level (i.e., PCEs are

not providing their intended recovery function) active restoration is needed to begin recovery of

the species.

Table 4 includes the functional level of habitat indicators for the sub-watershed in the action area

as assessed in the 2010 NRCS baseline analysis (NRCS 2010) and the project biological

assessment (MDT 2013, p. 9). Major effects to a habitat indicator results in a change in one

level of baseline condition (e.g. FA to FAR). Minor effects indicate the action may result in an

incremental or cumulative effect but does not result in a functional change to the system. For the

purposes of this checklist, restore (R) means to change the function of an indicator one condition

class (e.g. FUR to FAR). Maintain (M) means that the function of an indicator does not change,

and degrade (D) means to change the function of an indicator for the worse. In some cases, a

FUR indicator may be further degraded, and this should be noted.

Characteristics Subpopulation: This pathway is made up of subpopulation size, growth and

survival, life history diversity and isolation, and persistence and genetic integrity indicators. The

action will not affect the life history diversity and isolation, and persistence and genetic integrity

indicators. Direct mortality of bull trout could occur during construction project activities by

crushing an adult or juvenile bull trout. However, the section of river within the project area is

higher in gradient, flowing through a confined canyon. As such, much of this section is utilized

primarily as a migratory corridor (GEI Consultants 2013).

Water Quality: Water temperature, sedimentation, and chemical contamination/nutrients make

up the indicators for water quality. The proposed action will not affect water temperature or

spawning and rearing habitat. Increases in sedimentation from the action could temporarily

reduce the availability, quality, and abundance of substrate needed for macroinvertebrate

31

production. Fine sediment may also limit access to substrate interstices that provide important

cover during rearing and over-wintering periods (Goetz 1994 and Jakober et al. 2000). These

impacts will likely last only a few months as spring flows flushed sediment downstream.

The proposed action may result in short term increases in sediment due to general construction

activities. High levels of suspended sediment and turbidity can result in direct mortality of fish

by damaging and clogging gills (Curry and MacNeill 2004, p. 140). Fish gills are delicate and

easily damaged by abrasive silt particles (Bash et al. 2001i, p. 15). Fish are more susceptible to

increased suspended sediment concentrations at different times of the year or in watersheds with

naturally high sediment such as glaciated streams. Fish secrete protective mucous to clean the

gills (Erman and Ligon 1985, p. 18). In glaciated systems or during winter and spring high flow

conditions when sediment concentrations are naturally high, the secretion of mucous can keep

gills clean of sediment. Protective mucous secretions are inadequate during the summer months,

when natural sediment levels are low in a stream system. Consequently, sediment introduction at

this time may increase the vulnerability of fish to stress and disease (Bash et al. 2001g, p. 12).

Newcombe and Jensen (1996) have shown that construction effects upon fish are based on

suspended sediment mg/L over time expressed as duration in hours or days. Past monitoring

efforts indicate that total suspended sediment levels, elevated during the construction activity can

quickly (within 1 to 3 hours post construction) return to pre activity levels. The duration and

magnitude of sediment load increases during instream construction reflect watercourse size,

volume of flow, construction activity, effectiveness of Best Management Practices and sediment

particle sizes. The dispersion of suspended sediment concentrations within the plume will reflect

the flow conditions of the receiving waterbody (Julien, 1995). Very low flow conditions can

result in minimal dilution and high suspended solid concentrations. However, the distance of

downstream transport may be minimized. At the other extreme, high flows associated with

storm events can increase background levels and entrain exposed sediment at the crossing

location. Additionally, the downstream extent and concentrations of the sediment plume will

reflect the particle sizes of the material excavated. In this case, gravel and coarse sand will settle

out downstream close to the project site. Physical structures (BMP’s) such as silt curtains or

debris dams and boulders that trap particles promote the settling of suspended sediment.

Based upon the potential presence of bull trout in this stretch of the Thompson River, the

potential for localized short-term sediment effects to adult and juvenile bull trout may occur.

These impacts will be minimized through implementation of erosion control conservation

measures (MDT 2013, p. 15-16).

32

Table 4. Checklist for documenting the environmental baseline (NRCS 2010, MDT 2013) and

effects of the actions. The numbers following the habitat indicators correspond to the PCEs.

Pathways:

Indicators

Thompson River-Goat

Creek, Sub –watershed

(170102130407)

Major Effects of

the Actions

Minor Effects of

the Actions

FA/FAR/FUR M/D/R* M/D/R* Characteristics Subpopulation: Subpopulation Size FAR M M

Growth & Survival FAR M M

Life History Diversity & Isolation FAR M M

Persistence and Genetic Integrity FAR M M

Water Quality: Temperature 2, 3, 5, 8 FAR M M

Sediment 2, 3, 6, 8 FUR M D

Chemical Contam. / Nutrients 1, 2, 3, 8 FAR M D

Habitat Access: Physical Barriers 1, 2, 3, 9 FA M D

Habitat Elements: Substrate Embeddeness 1, 3, 6 FUR M M

Large Woody Debris 4, 6 FAR M M Pool Frequency & Quality 3, 4, 6 FAR M M Large Pools 4, 5 FAR M M Off-Channel Habitat 4 FAR M M Refugia 2, 5, 9 FUR M M

Channel Condition & Dynamics: Wetted Width/Max Depth Ratio 2, 4, 5 FAR M M Streambank Condition 1, 4, 5, 6 FAR M M Floodplain Connectivity 1, 3, 4, 5, 7, 8 FUR M M Flow & Hydrology: Change in Peak/Base Flows 1, 2, 5, 7 ,8 FAR M M

Drainage network Increase 1, 7, 8 FAR M M

Watershed Conditions: Road Density & Location 1, 5, 7 FUR M M

Disturbance History 4, 7, 8, 9 FUR M M

Riparian Conservation Area 1, 3, 4, 5, 7 FAR M M

Disturbance Regime 4, 7, 8 FAR M M

Integration of Species & Habitat Condition FUR M M

33

The proposed action has some potential for additions of toxic substances to the river that could

have long-term effects on macroinvertebrates production in the stream substrate and could

decrease available foraging habitat for bull trout. All construction equipment will be inspected

daily (during work days) to ensure hydraulic, fuel and lubrication systems are in good condition

and free of leaks to prevent these materials from entering any stream. Vehicle servicing and

refueling areas, fuel storage areas, and construction staging and materials storage areas will be

located a minimum of 50 feet from ordinary high water, typically referred to as the Q2 elevation,

and contained properly to ensure that spilled fluids or stored materials did not enter any stream.

Habitat Access: The following analysis is taken directly from the Department’s biological

assessment (MDT 2013, pp. 11-12). Scientific research by the Washington State Fish and

Wildlife Office in conjunction with the Washington Department of Transportation in April 2010,

indicate that impact pile-driving for the underwater installation of piers, pilings, etc., may result

in elevated underwater sound pressure waves that are physically detrimental to fish and other

animal species. The primary concern is that the sound pressure waves generated by impact pile

driving and other sources, such as explosives, can have negative physiological and neurological

effects on fish (Yelverton et al. 1973, Yelverton and Richmond 1981, Steevens et al. 1999,

Fothergill et al. 2001, U.S. Department of Defense 2002). Injury and mortality to fish species

has been directly attributed to impact pile-driving (Stotz and Colby 2001, Stadler 2002, Fordjour

2003, Abbott et al. 2005, Hastings and Popper 2005). In some instances, these high sound

pressure waves resulted in physical damage to the gas-filled internal organs of fish, such as

kidneys, eyes, and swim bladders (Turnpenny and Nedwell 1994, Turnpenny et al. 1994, Popper

2003, Hastings and Popper 2005). These injuries can occur as the result of barotraumas,

pathologies associated with high sound levels, including hemorrhage and rupture of internal

organs (Turnpenny and Nedwell 1994, Turnpenny et al. 1994, Popper 2003, Hastings and Popper

2005).

Essentially, the sound waves enter the fish tissue as the tissues nearly match the surrounding

water’s acoustical behavior (Hastings 2002). When the sound waves pass through the fish, they

cause the swim bladder to rapidly contract and expand repeatedly with the high sound pressure

waves of the impact pile driving. This rapid expansion and contraction of the swim bladder

causes it to repeatedly batter the surrounding internal tissues and organs, such as the kidneys,

heart, liver, etc. (Gaspin 1975). Yelverton and others have found that body mass factors into the

effect of sound pressure waves on fish, whereby fish greater in mass and size would require a

greater impulse level of sound to cause an injury, while fish with a smaller mass and size would

sustain injuries from smaller impulses. For the purpose of endangered species consultations, and

until new information becomes available to refine the criteria, NOAA Fisheries expects the onset

of physical injury would occur if either the peak sound pressure level (SPL) exceeds 206 dB (re:

1µPa) or the SEL, accumulated of all pile strikes generally occurring within a single day,

exceeds 187 dB (re: 1 µPa2·sec) for fishes 2 grams or larger, or 183 dB for smaller fishes

(Stadler and Woodbury 2009).

The most noticeable and documented effects resulting from impact pile-driving is fish kills, but it

is reported that not all fish killed by pile driving float to the surface, and thus remain undetected

(Telecki and Chamberlain 1978, WSDOT 2003). Death resulting from barotraumas did not

necessarily result in immediate death, as it occurred within minutes to days after exposure to

34

these sound pressure waves (Abbott et al. 2002). Dependent on the source of such underwater

sound pressure levels, they can also result in temporary stunning of fish, and alterations in

behavior that could potentially affect fish feeding and predator evasion within the vicinity of the

pile driving activity (Turnpenny and Nedwell 1994, Turnpenny et al. 1994, Popper 2003,

Hastings and Popper 2005).

During the proposed project, contractors may construct temporary work bridges through

pounding temporary pilings and sheet piling coffer dams in the active channel for temporary

piers. The installation of the temporary piers and coffer dams using pile-driving technology

could have detrimental impact on bull trout within the immediate project area, if it occurs when

the potential for bull trout presence is highest. Hence, the proposed project may cause a

temporary physical and behavioral barrier to adult or juvenile bull trout in the river system due to

construction activities, such as work bridge installation, existing bridge demolition, and

installation and removal of coffer dams. These temporary barrier effects would last until the

temporary facilities are removed and the project is completed (MDT 2013).

Habitat Elements and Channel Condition and Dynamics: The habitat elements pathway

consists of the following six indicators: substrate embeddedness, large woody debris, pool

frequency and quality, large pools, off-channel habitat, and refugia. Habitat indicators wetted

width/max depth ratio, streambank condition, and floodplain connectivity are the three indicators

that make up the channel condition and dynamics pathway. No effects are anticipated to this

pathway from the proposed action.

B. Species Response to the Proposed Action

The project has potential to directly affect adult and sub-adult bull trout from increased turbidity

due to intermittent instream activities, through behavioral effects, abandonment of cover, short-

term reductions in feeding rates and success, and minor physiological stress (U.S. Fish and

Wildlife Service 2010). However, population numbers in the action area are low, and the

Service does not anticipate impacts associated with increases in turbidity would rise to the level

of take due to the expected sediment dose (exposure).

Intermittent, temporary barriers due to sound pressure waves from pile-driving, and potential

temporary physical barriers from demolition of the existing bridge, have limited potential to

harm and harass juvenile and adult bull trout that may be in the project area, due to low

population numbers in the action area. Despite the low population numbers in the action area,

there is the chance that an individual fish may be affected and temporarily avoid, or be

physically prevented from, migrating up or downstream until construction activities: (1) cease

for the day, (2) the temporary construction impacts associated with the temporary facilities are

removed and the project is complete, or (3) debris from the demolished bridge is removed from

the channel.

For indirect effects, the new bridge is designed to prevent stormwater runoff including de-icing

chemicals, road debris, and sanding materials from directly entering the Thompson River.

Bridge deck runoff will be directed to the bridge ends where runoff will be filtered through

vegetated swales and/or riprap chutes which end prior to entering the river. Some riparian trees

35

and shrubs will be removed with the construction of the new bridge and roadway approaches

adjacent to the bridge. The following stream functions/factors should remain the same as

currently exist: sediment transport capacity, channel stability, width depth ratio, substrate

composition, and the limited pool habitat for bull trout. The proposed project should not have

any long-term effects on water quality, long-term stream function, nor will it deter fish, such as

bull trout, from returning to this reach of the Thompson River once the project and all

construction activities have been completed (MDT 2013).

B.1 Effects of the Action to Designated Critical Habitat

The specific effects of the proposed action on critical habitat are virtually the same as those

described in the preceding section, because the PCEs considered under critical habitat involve

the same habitat parameters analyzed in the matrix (Table 4). Consequently, those discussions

and analysis of effects apply here; and therefore, will not be repeated. The primary factor by

which bull trout and bull trout critical habitat have the potential to be adversely affected by the

proposed action is through changes to habitat indicators sediment (turbidity PCE 8) and physical

barriers (PCE 2 physical barriers).

Bull Trout Critical Habitat within the project area will be affected in the same way and to the

same degree as listed and discussed in the matrix and rationale sections above. In the short-term,

critical habitat will be adversely affected through increased embeddedness of substrates

downstream of the project site until the next high water event. Because increased sediment

levels due to instream and incidental construction activities are not expected to exceed 148 mg/L

over a three hour time period (MDT 2013), the associated impacts to bull trout critical habitat

would not be expected to rise to the level of take (U.S. Fish and Wildlife Service 2010).

Impacts from sound pressure waves from pile-driving and its effectiveness as a barrier to

movement may occur from the activity (e.g., pile-driving of temporary piers for work bridges).

As a result, barring physical impedance of the sound pressure waves (e.g., river bends, gravel

bars, boulders, etc.), a bull trout may be physically affected by pile-driving activities. As a

result, during pile-driving activities, impacts to bull trout movement within the project area may

be affected, resulting in a short-term minor degrade to PCE 2. Additionally, during demolition

of the existing bridge, as the structure is cut up for removal, portions of the structure may enter

the wetted channel and present temporary (3 to 5 days) partial or complete barriers to fish

passage within the action area. Thus, once construction activities are completed, it is expected

that PCE 2 will be restored to current conditions.

The impacts associated with this project are not discountable, insignificant, or entirely beneficial.

The proposed action would result in a short-term contribution to the overall risk to bull trout

critical habitat in the Lower Clark Fork River CHSU. Due to the scale of the project-related

effects in relation to the entire Clark Fork CHU, there is an extremely low probability that the

Thompson River East project would result in destruction or adverse modification of proposed

critical habitat for bull trout at the scale of the Columbia River IRU.

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VII. Cumulative Effects

Cumulative effects include the effects of future state, tribal, local or private actions that are

reasonably certain to occur in the action area considered in this biological opinion. Future

federal actions that are unrelated to the action are not considered in this section because they

require separate consultation pursuant to section 7 of the Act.

The Lower Clark Fork River Core Area Assessment (USDI 2008) identified several risks to bull

trout in the Lower Clark Fork core area including: fish passage issues (artificial barriers to

migration), non-native species, forest management practices and forest roads, entrainment

(hydropower and diversions), water quality, and dewatering.

Within the Thompson River drainage, landownership is roughly divided as 47 percent Lolo

National Forest, 43 percent Plum Creek, 7 percent Montana Department of Natural Resources

and Conservation (MTDNRC), and 3 percent private inholdings. The lower third of the

Thompson River drainage is primarily owned by the Lolo National Forest; the middle third is

generally a checkerboard division of Lolo National Forest, Plum Creek, and MTDNRC

landownership; and the upper third is primarily Plum Creek and other private lands (GEI

Consultants 2013). Within this MTDNRC and Plum Creek have each developed and are

implementing Habitat Conservation Plans (HCPs) to protect native fish relative to forest

management and associated actions. The MTDNRC HCP was completed in 2011, and the Plum

Creek Native Fish HCP was completed in 2000, and each should improve habitat values for bull

trout in the action area.

In 2008, as part of the Federal Energy Regulatory Commission (FERC) relicensing process for

the Thompson Falls Dam by PPL Montana, the Service filed a biological opinion (USDI 2008b)

and associated Incidental Take Statement, which included reasonable and prudent measures and

Terms and Conditions to minimize incidental take of bull trout. The Service’s Terms and

Conditions 2 stated that PPL Montana would provide annual funding for a technical advisory

committee (TAC) to conduct offsite habitat restoration or acquisition in important upstream bull

trout spawning and rearing tributaries, with the purpose of boosting recruitment of juvenile bull

trout. From 2009 until January 2013, the TAC has funded 11 such projects. This work is

expected to continue through 2020 (GEI Consultants 2013, USDI 2008b).

Cumulative effects within the core areas are reflected in bull trout population numbers and life

history forms. All core areas are at risk of increased activities and concern for the viability and

effects to bull trout populations well documented (USDI 2005). Clearly, activities occurring

instream within channels on private lands at the same time these federal activities occurred on

the same stream will result in additive adverse effects to bull trout, at least in the short-term.

However, some non-federal activities will likely also be targeted for improving conditions for

bull trout from existing levels over the long-term and will work in concert with federal actions

toward recovery of bull trout in some instances.

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VIII. Conclusion

Jeopardy Analysis of Columbia Basin Bull Trout Population

After reviewing the current status of bull trout, the environmental baseline (including effects of

Federal actions covered by previous biological opinions) for the action area, the effects of the

proposed road management actions, and the cumulative effects, it is the Service’s biological

opinion that the actions as proposed, are not likely to jeopardize the continued existence of bull

trout. This conclusion is based on the magnitude of the project effects (to reproduction,

distribution, and abundance) in relation to the listed population. Implementing regulations for

section 7 (50 CFR 402) define “jeopardize the continued existence of” as to “engage in an action

that reasonably would be expected, directly or indirectly, to reduce appreciably the likelihood of

both the survival and recovery of a listed species in the wild by reducing the reproduction,

numbers, or distribution of that species.” Our conclusion that the proposed action will not

jeopardize the continued existence of bull trout is based primarily on the information and

analyses in this biological opinion, and information presented in the biological assessment for the

proposed action (MDT 2013).

Jeopardy determinations for bull trout are made at the scale of the listed entity, which is the

coterminous United States population (64 FR 58910). This follows the April 20, 2006, analytical

framework guidance described in the Service’s memorandum to Ecological Services Project

Leaders in Idaho, Oregon and Washington from the Assistant Regional Director – Ecological

Services, Region 1 (USDI 2006). The guidance indicates that a biological opinion should

concisely discuss all the effects and take into account how those effects are likely to influence

the survival and recovery functions of the affected interim recovery unit(s), which should be the

basis for determining if this action was “likely to appreciably reduce both survival and recovery

of the coterminous United States population of bull trout in the wild.”

As discussed earlier in this biological opinion (see Part III.), the approach to the jeopardy

analysis in relation to the action follows a hierarchal relationship between units of analysis (i.e.,

geographical subdivisions) that characterize effects at the lowest unit or scale of analysis (the

local population) toward the highest unit or scale of analysis (the Columbia River Interim

Recovery Unit) of analysis. The hierarchal relationship between units of analysis (local

population, core areas) is used to determine whether the action was likely to jeopardize the

survival and recovery of bull trout. As mentioned previously, should the adverse effects of the

action not rise to the level where it appreciably reduces both survival and recovery of the species

at a lower scale, such as the local or core population, the action could not jeopardize bull trout in

the coterminous United States (i.e., rangewide). Therefore, the determination would result in a

no-jeopardy finding. However, should an action cause adverse effects that are determined to

appreciably reduce both survival and recovery of the species at a lower scale of analysis (i.e.,

local population), then further analysis is warranted at the next higher scale (i.e., core area).

Our conclusion is based on the magnitude of the project effects in relation to the Lower Clark

Fork core area bull trout population. Our rationale for this no jeopardy conclusion is based on

the following:

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The implementation of the proposed action is not anticipated to reduce the reproduction,

numbers, or distribution of bull trout within the Lower Clark Fork River core area or

action area to the degree that survival or recovery is reduced.

As a result, the Service concludes that implementation of this project is not likely to appreciably

reduce both the survival and recovery of bull trout at the Lower Clark Fork core area, and by

extension, the Clark Fork River Management Unit. Therefore, the Service concludes the action

will not jeopardize the continued existence of bull trout within the coterminous United States

population of the bull trout.

Adverse modification of bull trout critical habitat analysis

After reviewing the current status of the Lower Clark Fork core area of bull trout and its

relationship to the Upper Columbia River bull trout population, the environmental baseline for

the action area, the effects of the action, and cumulative effects, it is the Service's opinion the

actions as implemented are not likely to destroy or adversely modify the bull trout critical

habitat. The Service defines destruction or adverse modification as “a direct or indirect alteration

that appreciably diminishes the value of critical habitat for both the survival and recovery of a

listed species. Such alterations include, but are not limited to, alterations adversely modifying

any of those physical or biological features that were the basis for determining the habitat to be

critical.” However, recent decisions by the 5th

and 9th

Circuit Court of Appeals have invalidated

this definition. Pursuant to current national policy and the statutory provisions of the Act,

destruction or adverse modification is determined on the basis of whether, with implementation

of the action, the affected critical habitat would remain functional (or retain the current ability for

the primary constituent elements to be functionally established) to serve the intended

conservation role for the species.

The proposed project is likely to adversely affect PCEs 2, 3, and 8. These impacts are small

relative to the amount of FMO in the Lower Clark Fork CHSU (189 miles), and localized along

0.36 miles of the river. The Service anticipates that critical habitat within the action area CHSU

will retain the current ability for the PCEs to be functionally established in the Lower Clark Fork

CHSU. By extension the project as implemented is not likely to adversely modify the Clark

Fork River Critical Habitat Unit, and as a whole will remain functional.

INCIDENTAL TAKE STATEMENT

Section 9 of the Act and Federal regulation pursuant to section 4(d) of the Act prohibit the take

of endangered and threatened species, respectively, without special exemption. Take is defined

as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to

engage in any such conduct. Harm is further defined by the Service to include significant habitat

modification or degradation that results in death or injury to listed species by significantly

impairing essential behavioral patterns, including breeding, feeding, or sheltering. Harass is

defined by the Service as intentional or negligent actions that create the likelihood of injury to

listed species to such an extent as to significantly disrupt normal behavior patterns which

include, but are not limited to, breeding, feeding or sheltering. Incidental take is defined as take

39

that is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity.

Under the terms of section 7(b)(4) and section 7(o)(2), taking that is incidental to and not

intended as part of the agency action is not considered to be prohibited taking under the Act

provided that such taking is in compliance with the terms and conditions of this Incidental Take

Statement.

The measures described below are not discretionary and must be undertaken by the

Administration and the Department so that they become binding conditions of any contract issued

to a road contractor, as appropriate, for the exemption in section 7(o)(2) to apply. The

Administration has a continuing duty to regulate and oversee the activity covered by this

Incidental Take Statement. If the Administration and Department fail to assume and implement

the terms and conditions of the Incidental Take Statement, the protective coverage of section

7(o)(2) may lapse. To monitor the impact of incidental take, the Administration and Department

must report the progress of the action and its impact on the species to the Service as specified in

the Incidental Take Statement [50 CFR 402.14(i)(3)].

Amount or Extent of Take Anticipated

The Service anticipates that project activities will result in incidental take of bull trout in the

form of harm, harassment or mortality related to the short-term degradation of aquatic habitat

parameters related to increased levels of activity-created sediment, physical barriers, and the

related risk to bull trout life history stages. Activity-created sediment, when additively combined

with increased background sediment, may impact bull trout habitat indicators including sediment

and substrate embeddedness. Sedimentation from the proposed activity will have short-term

adverse effects (sub-lethal) by impairing feeding and sheltering patterns of juvenile and adult

bull trout to the extent of injury (harm and/or harassment). In addition the Service expects a low

level of take from the temporary reduction of habitat function (i.e. minor degrades FAR habitat

indicators) over the long-term. Reductions in these habitat pathways will likely impair feeding

and sheltering patterns of juvenile and adult bull trout to the extent that injury (harm and/or

harassment) may occur. Sound pressure waves resulting from pile-driving and blasting activities

would be expected to temporarily create a temporary physical barrier preventing the movement

of bull trout through the project area for the duration of the pile-driving or blasting activity.

Furthermore, pile-driving activities may harass individual bull trout from the project area,

disrupting normal behavior patterns which include, but are not limited to, breeding, feeding or

sheltering. Finally, depending upon bull trout proximity to the pile-driving and blasting

activities, the sound pressure waves may induce barotraumas to individuals, possibly resulting in

physical harm or mortality. Because of the low population levels of bull trout within the action

area, the Service anticipates a low level of take from the proposed action over the long-term.

Additionally, during the demolition of the existing structure, portions of the structure may fall

into the active channel and present partial or complete barriers to fish passage for up to 3 to 5

days. The temporary obstructions may harass individual bull trout from the project area,

disrupting normal behavior patterns which include, but are not limited to, breeding, feeding or

sheltering. Because of the low population levels of bull trout within the action area, the Service

anticipates a low level of take from the proposed action over the long-term. The amount of take

that may result from implementation of the action is difficult to quantify for the following

reasons:

40

The amount of sediment produced or delivered is determined by a number of factors that

are not only influenced by local site parameters such as topography and soil type, but are

influenced by weather, time of implementation and effectiveness of the mitigation

measures.

The amount and location of sediment deposition depends on numerous factors (e.g. flow

regime, size of stream, channel roughness).

Losses may be masked by seasonal fluctuations in numbers, and aquatic habitat

modifications are difficult to ascribe to particular sources, especially in already degraded

watersheds.

Because of the wide ranging distribution of bull trout, identification and detection of dead

or impaired species, and not all barotrauma-induced mortalities float to the surface,

detection of injured or dead individuals may be difficult.

For these reasons, the Service has determined that the actual amount or extent of the anticipated

incidental take is difficult to determine. In these cases, the Service uses surrogate measures to

measure the amount or extent of incidental take, and determine when the amount of take

anticipated has been exceeded. In this biological opinion we use length of occupied stream

affected (1,900 feet), and the duration of the project (24 months).

The Service anticipates that incidental take of bull trout will occur intermittently in the

Thompson River from the Thompson River Bridge approximately 600 feet upstream and 1,300

feet downstream. Take would be expected to occur when pile-driving and bridge demolition

activities occur. This portion of the Thompson River is used primarily as a migratory corridor

for bull trout (GEI Consultants 2013), however, it also supports adult and juvenile bull trout and

foraging overwintering and migratory habitat. Thus, the take would apply to juvenile and adult

bull trout within the project area. If at any time during implementation of the project, the

Administration and Department conducts pile-driving or blasting activities in addition to those

described in the proposed action, or conducts proposed activities in a manner that differs from

that described in the proposed action, then the amount of take we anticipate would be exceeded.

Effect of the Take

In the accompanying biological opinion, the Service determined that the extent and type of take

described is not likely to jeopardize the continued existence of bull trout in the Lower Clark Fork

core area or the Columbia River Distinct Population Segment/Interim Recovery Unit.

Reasonable and Prudent Measures

Incidental take statements typically provide reasonable and prudent measures which are expected

to reduce the amount of incidental take. Reasonable and prudent measures are those measures

necessary and appropriate to minimize the incidental take resulting from the proposed action.

These reasonable and prudent measures are non-discretionary and must be implemented by the

41

Administration in order for the exemption in section 7(0)(2) to apply. The Service believes the

following reasonable and prudent measure(s) are necessary and appropriate to minimize impacts

of incidental take of bull trout.

1. The Administration and the Department shall identify and implement means to reduce the

potential for incidental take of bull trout from harassment, harm, and direct mortality in the

Thompson River as a result of construction related activities associated with this project.

2. The Administration and the Department shall monitor approach construction and bridge

replacement activities (including bridge demolition and removal, channel manipulation, and

revegetation activities) to ensure that these activities comply with the biological assessment,

supporting documentation, and biological opinion for this project. The Administration and the

Department shall also implement the reporting requirement as described in the terms and

conditions below.

Terms and Conditions

The following terms and conditions implement the reasonable and prudent measures as described

above.

1. To fulfill reasonable and prudent measure #1 the following terms and conditions shall be

implemented:

a). Pile-driving each pipe and sheet pile shall initiate with lower hammer lifts than are

required for the task for the initial six strikes to reduce the initial sound exposure level

(SEL), to encourage fish to vacate the surrounding area, and reduce the risk of

barotraumas and mortality, or use a vibratory hammer.

b). To the maximum extent possible, the existing bridge will be disassembled and

removed without pieces being allowed to fall into the stream. If portions of the old

bridge do fall into the stream during demolition, they will be removed from the stream

without dragging the material along the streambed. Any blasting required to knock the

center truss off of the piers will be contained to the maximum extent possible using some

type of containment shielding device to attenuate the blast’s pressure wave in the water

and to prevent debris from entering the stream.

c). Instream work conducted within the Thompson River channel shall be kept to the

minimum amount necessary, preferably during periods of low flow. This includes, but is

not limited to, construction and removal of any coffer dams that may be needed for the

driving and removal of pilings for any temporary support structures that may be

necessary. Instream construction work shall be completed in the shortest amount of time

possible.

d). Instream work should be kept to the absolute minimum amount necessary. Any

temporary work or detour bridges necessary at these crossings should clear span the

stream channel, if possible. No construction equipment should be allowed to operate

42

within the active channel of any stream unless permitted to do so. If at all possible,

schedule instream construction activities such that as many of the necessary construction

activities as possible occur “in the dry.”

e). Should instream activities displace channel features (e.g., large woody debris,

boulders, etc.), the Administration and Department shall restore the channel to the

conditions that existed prior to project commencement.

f). Materials excavated from inside any coffer dams shall not enter any stream.

g). Best management practices for erosion control shall be applied to this project,

including:

Constructing silt fencing to prevent sediment from reaching water bodies;

Using straw bales in borrow ditches to prevent erosion and sediment transport;

Quickly reseeding and revegetating all disturbed areas with native vegetation,

including embankments and borrow ditches, and adding a woody vegetation

component to the riparian revegetation plans;

Using bank stabilization measures for disturbed channel banks; and

Maintaining and protecting riparian vegetation to the maximum extent possible

within the construction zone.

h). All waste fuels, lubricating fluids, herbicides, and other chemicals will be collected

and disposed of in a manner that ensures that no adverse environmental impact will

occur. Construction equipment will be inspected daily to ensure hydraulic, fuel and

lubrication systems are in good condition and free of leaks to prevent these materials

from entering any stream. Vehicle servicing and refueling areas, fuel storage areas, and

construction staging and materials storage areas will be sited and contained properly to

ensure that spilled fluids or stored materials do not enter any stream.

2. To fulfill reasonable and prudent measure #2, the following terms and conditions shall be

implemented:

a). Structures designed to minimize sediment and pollutant runoff from sensitive areas

such as settling ponds, vehicle and fuel storage areas, hazardous materials storage sites,

erosion control structures, and coffer dams shall be visually monitored daily, especially

following precipitation events, to ensure these structures are functioning properly.

b). The construction zones within coffer dams will be visually checked during dewatering

activities to ensure bull trout are not trapped. In the unlikely event a bull trout is found

within a coffer dam, it will immediately be returned to the stream.

c). Upon locating dead, injured or sick bull trout, notification must be made within 24

hours to the Service’s Montana Field Office at (406)449-5225. Record information

relative to the date, time and location of dead or injured bull trout when found, and

possible cause of injury or death of each fish and provide this information to the Service.

43

d). The Administration and Department shall provide an annual report by December 31

each year detailing project progress, deviations from design, extent of revegetation

efforts, and survival rates of plantings. Monitoring and reporting of revegetation efforts

within the riparian zone will continue for three years post-construction, with a target of

80% survival of plantings three years after planting.

The reasonable and prudent measures, with their implementing terms and conditions, are

designed to minimize the impact of incidental take that might otherwise result from the proposed

action. With implementation of these measures, the Service expects that take of bull trout will be

limited to harm or harassment and the resulting impacts to instream habitat associated with

bridge construction and removal activities. If, during the course of the action, term and condition

#1 outlined above is not adhered to, the level of incidental take anticipated in this biological

opinion may be exceeded. Such incidental take represents new information requiring reinitiation

of consultation and review of the reasonable and prudent measures provided. The Federal

agency must immediately provide an explanation of the causes of the taking and review with the

Service the need for possible modification of the reasonable and prudent measures.

Conservation Recommendations

Section 7(a)(1) of the Act directs Federal agencies to utilize their authorities to further the

purposes of the Act by carrying out conservation programs for the benefit of endangered and

threatened species. Conservation recommendations are discretionary agency activities to

minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to

help implement recovery programs, or to develop information.

1. To reduce potential impact on migrating bull trout, the Service recommends demolition of the

existing bridge superstructure occur during the Thompson River’s low flow period (July 15 –

September 30). Adherence to this time period would reduce the impact to migrating bull trout

from temporary partial or complete channel barriers due to pieces of the existing bridge entering

the Thompson River.

2. To assist in meeting the Department’s responsibilities under Section 7(a)(1) of the Act, and to

utilize authorities granted within the Moving Ahead for Progress in the 21st Century (MAP-21)

Act, which provide opportunities to increase partnerships between transportation and

environmental sectors, the Service strongly recommends that the Department work proactively

with the Service, Montana Department of Fish, Wildlife and Parks, and others to identify and

remedy any impacts to salmonids, including bull trout, within the Lower Clark Fork core area

that are the result of transportation systems. Within this area, many streams were channelized

during road and railroad construction, resulting in shortening of stream channels, increased

erosion, higher water velocities, and loss of fish habitat. In addition, there is a risk of future

toxic spills occurring and materials entering these streams.

3. The Service recommends the Department explore potential opportunities to utilize their

expertise and authorities to promote innovative and non-traditional fisheries enhancement

projects within the Lower Clark Fork core area by partnering in some manner with other

agencies or groups to conduct a comprehensive analysis of the impacts of transportation systems

44

on Clark Fork River channel morphology, and identify potential opportunities for corrective

measures. The draft Bull Trout Recovery Plan recommends many recovery tasks that need to be

accomplished to protect, restore, and maintain suitable habitat conditions for bull trout in this

area. The Service supports efforts to reconnect meander bends, and improve floodplain

connectivity throughout the Clark Fork River.

In order for the Service to be kept informed of actions minimizing or avoiding adverse effects or

benefiting listed species or their habitats, the Service requests notification of the implementation

of any conservation recommendations.

Reinitiation Notice

This concludes formal consultation on the action outlined in your April 9, 2013, request for

consultation. As provided in 50 CFR §402.16, reinitiation of formal consultation is required

where discretionary Federal agency involvement or control over the action has been retained (or

is authorized by law) and if: (1) the amount or extent of incidental take is exceeded; (2) new

information reveals effects of the agency action that may affect listed species or critical habitat in

a manner or to an extent not considered in this opinion; (3) the agency action is subsequently

modified in a manner that causes an effect to the listed species or critical habitat that was not

considered in this opinion; or (4) a new species is listed or critical habitat designated that may be

affected by the action. In instances where the amount or extent of incidental take is exceeded,

any operations causing such take must cease pending reinitiation.

45

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habitat in the upper Yellowstone River. Draft Executive Summary for the Governor’s Upper

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Brewin, P.A. and M.K. Brewin. 1997. Distribution for bull trout in Alberta. Pp. 209-216 in

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46

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Appendix A.

Crosswalk between the Bull Trout Matrix of Pathways and Indicators (MPI) and Primary

Constituent Elements (PCEs) of Critical Habitat

The Matrix of Pathway Indicators (framework) for bull trout is used to evaluate and document

baseline conditions and to aid in determining whether a project is likely to adversely affect or

result in the incidental take of bull trout.

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The MPI analysis incorporates 4 population indicators and 19 physical habitat indicators.

Analysis of the habitat indicators can provide a thorough evaluation of the existing baseline

condition and potential project impacts to the PCEs of proposed critical habitat for bull trout.

Table 1 shows the relationship between the PCEs for bull trout critical habitat and the MPI

habitat indicators.

The following paragraphs describe how the MPI indicators are related to evaluating the function

of each PCE for proposed bull trout critical habitat.

1. Springs, seeps, groundwater sources, and subsurface water connectivity (hyporehic

flows) to contribute to water quality and quantity and provide thermal refugia.

The analysis of floodplain connectivity considers the hydrologic linkage of off-channel

areas with the main channel and overbank-flow maintenance of wetland function and

riparian vegetation and succession. Floodplain and riparian areas provide hydrologic

connectivity for springs, seeps, groundwater upwelling and wetlands and contribute to the

maintenance of the water table. The analysis of changes in peak/base flows addresses

subsurface water connectivity and substrate embeddedness addresses inter-gravel flows.

Increase in drainage network and road density and location address potential changes to

groundwater sources and subsurface water connectivity. Streambank condition,

floodplain connectivity and riparian conservation areas address groundwater influence.

Chemical contamination/nutrients addresses concerns regarding groundwater water

quality.

2. Migratory habitats with minimal physical, biological, or water quality impediments

between spawning, rearing, overwintering, and freshwater and marine foraging

habitats, including but not limited to permanent, partial, intermittent, or seasonal

barriers.

Physical, biological or chemical barriers to migration are addressed directly through

water quality habitat indicators, including temperature, sediment, chemical

contamination/nutrients and physical barriers. The analysis of these indicators assess

whether barriers have been created due to impacts such as high temperatures or high

concentrations of turbidity or contaminants. Analysis of change in peak/base flows and

average wetted width/maximum depth ratio assess whether changes in flow might create

a seasonal barrier to migration. An analysis of refugia considers the habitat’s ability to

support strong, well distributed, and connected populations for all life stages and forms of

bull trout.

3. An abundant food base, including terrestrial organisms of riparian origin, aquatic

macroinvertebrates, and forage fish.

Floodplain connectivity and riparian conservation areas provide habitat to aquatic

invertebrates, which in turn provide a forage base for bull trout. Pool frequency and

quality and substrate embeddedness contributes to the variety and density of aquatic

invertebrates and other fish species. Changes in temperature, sediment, and chemical

contaminants and nutrients affect aquatic invertebrate production.floodplain and riparian

areas provide habitat to aquatic invertebrates, which in turn provide a forage base for bull

trout. The combined analyses of all the Matrix habitat indicators and the other seven

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PCEs provide information to assess whether there is an abundant food base in the

analysis area. Therefore, any impairment to the food base will be addressed by way of

summarizing the biological and habitat indicators.

4. Complex river, stream, lake, reservoir, and marine shoreline aquatic environments and

processes with features such as large wood, side channels, pools, undercut banks and

substrates, to provide a variety of depths, gradients, velocities, and structure.

Large woody debris increases channel complexity and creates pools and undercut banks,

so the analysis of the current amounts and sources of large woody debris available for

recruitment is pertinent to this PCE. Pool frequency and quality considers the number of

pools per mile as well as the amount of cover and temperature of water in the pools.

Average wetted width/maximum depth ratio is an indicator of channel shape and pool

quality. Low ratios suggest deeper, higher quality pools. Large pools, consisting of a

wide range of water depths, velocities, substrates and cover, are typical of high quality

habitat and are a key component of channel complexity. Analysis of off-channel habitat

describes side-channels and other off-channel areas. Streambank condition analyzes the

stability of the banks, including features such as undercut banks. The analysis of both

riparian conservation areas, and floodplain connectivity, disturbance history, and

disturbance regime includes the maintenance of habitat and channel complexity, the

recruitment of large woody debris, and the connectivity to off-channel habitats or side

channels. Complex habitats provide refugia for bull trout and in turn, analysis of refugia

assesses complex stream channels. All of these habitat indicators consider the numerous

characteristics of instream bull trout habitat and quantify critical components that are

fundamental to creating and maintaining complex instream habitat over time.

5. Water temperatures ranging from 2 to 15 °C (36 to 59 °F), with adequate thermal

refugia available for temperatures at the upper end of this range. Specific temperatures

within this range will vary depending on bull trout life-history stage and form;

geography; elevation; diurnal and seasonal variation; shade, such as that provided by

riparian habitat; and local groundwater influence.

This PCE is addressed directly by the analysis of temperature. It is also addressed

through consideration of refugia, which by definition is high quality habitat of

appropriate temperature. Availability of refugia is also considered in analysis of pool

frequency and quality and large pools. Average wetted width/maximum depth ratio is an

indication of water volume, which indirectly indicates water temperature, i.e., low ratios

indicate deeper water, which in turn indicates possible refugia. This indicator in

conjunction with change in peak/base flows is an indicator of potential temperature and

refugia concerns particularly during low flow periods. Streambank condition, floodplain

connectivity, road density and location and riparian conservation areas address the

components of shade and groundwater influence, both of which are important factors of

water temperature. Stable streambanks and intact riparian areas, which include part of the

floodplain, typically support adequate vegetation to maintain thermal cover to streams

during low flow periods. Road density and location addresses the potential contributions

of warm water discharges from stormwater ponds.

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6. Substrates of sufficient amount, size, and composition to ensure success of egg and

embryo overwinter survival, fry emergence, and young-of-the-year and juvenile

survival. A minimal amount (e.g., less than 12 percent) of fine substrate less than 0.85

mm (0.03 in.) in diameter and minimal embeddedness of these fines in larger

substrates are characteristic of these conditions.

The analyses for sediment and substrate embeddedness assess substrate composition and

stability in relation to the various life stages of the bull trout as well as the sediment

transportation and deposition. Large woody debris and pool frequency and quality affect

sediment transport and redistribution within a stream and assessment of these indicators

will clarify substrate composition and amounts. Analysis of streambank condition will

provide insight into the amount of fine sediment contribution.

7. A natural hydrograph, including peak, high, low, and base flows within historic and

seasonal ranges or, if flows are controlled, they minimize departures from a natural

hydrograph.

The analysis of change in peak/base flows considers changes in hydrograph amplitude or

timing with respect to watershed size, geology, and geography. Analyses of floodplain

connectivity, increase in drainage network, road density and location, disturbance

history, and riparian conservation areas provides further information regarding possible

interruptions in the natural stream hydrology. Floodplain connectivity considers the

hydrologic linkage of off-channel areas with the main channel. Roads and vegetation

management both have effects strongly linked to a stream’s hydrograph. Disturbance

regime ties this information together to consider how a watershed reacts to disturbance

and the time required to recover back to pre-disturbance conditions.

8. Sufficient water quality and quantity such that normal reproduction, growth, and

survival are not inhibited.

The quantity of permanent water will be considered in the analyses for PCE 4 natural

hydrograph and PCE 5 springs, seeps, and groundwater, which include floodplain

connectivity, changes in peak/base flows, drainage network increase, disturbance history,

and disturbance regime. Analysis of temperature, sediment, and chemical contaminates

and nutrients consider the quality of permanent water. Current listing under 303(d) and

305(d) status should be considered, as well as the causes for that listing. Analysis

pertinent to sediment should address turbidity.

9. Few or no nonnative predatory (e.g., lake trout, walleye, northern pike, smallmouth

bass; inbreeding (e.g., brook trout); or competitive (e.g., brown trout) species present.

This PCE is not well covered by existing MPI analyses. Some information may be

available from analyses of population indicators, particularly the “persistence and genetic

integrity” indicator.

Table 1. MPI indicators relevant to each of the Primary Constituent Elements of

proposed bull trout critical habitat (2010 version).

Diagnostic Pathway/Indicator

*PCE 1 -

Springs, seeps,

groundwater

PCE 2 -

Migratory

Habitats

PCE 3 -

Abundant

food base

PCE 4 -

Complex

habitats

PCE 5 -

Water

Temperature

PCE 6 -

Substrate

features

PCE 7 -

Natural

Hydrograph

PCE 8 -

Water quality

and quantity

PCE 9 -

Predators and

competitors

Water Quality

Temperature x x x x

Sediment x x x x

Chemical Contaminants and Nutrients x x x x

Habitat Access

Physical Barriers x x x x

Habitat Elements

Substrate Embeddedness x x x

Large Woody Debris x x

Pool Frequency and Quality x x x

Large Pools x x

Off-Channel Habitat x

Refugia x x x

Channel Conditions and Dynamics

Wetted Width/Maximum Depth Ratio x x x

Streambank Condition x x x x

Floodplain Connectivity x x x x x x

Flow/Hydrology

Changes in Peak/Base Flows x x x x x

Drainage Network Increase x x x

Watershed Conditions

Road Density and Location x x x

Disturbance History x x x x

Riparian Conservation Areas x x x x x

Disturbance Regime x x x

*Updated for 2010 proposed rule Khalupka

2-24-10