Distribution and Abundance of Rainbow Trout/Steelhead and ... BC/Clear Creek Monitoring Final Reports... · Clear Creek Adult Rainbow Trout/steelhead and Late-fall run Chinook; winter

Distribution and Abundance of Rainbow Trout/Steelhead and Late-fall Run

Chinook Salmon Redds in Clear Creek; Winter 2016 to Spring 2017

Prepared by:

Samuel S. Provins

Charles D. Chamberlain

U.S. Fish and Wildlife Service

Red Bluff Fish and Wildlife Office

10950 Tyler Road

Red Bluff, CA 96080

September 2019

U.S Fish and Wildlife Service Red Bluff Fish and Wildlife Office

Clear Creek Adult Rainbow Trout/steelhead and Late-fall run Chinook; winter 2016 to spring 2017 ii

Disclaimer

The mention of trade names or commercial products in this report does not constitute

endorsement or recommendation for use by the federal government.

The correct citation for this report is:

Provins S.S. and C.D. Chamberlain. 2019. Distribution and abundance of Rainbow

Trout/steelhead and late-fall run Chinook Salmon redds in Clear Creek; winter 2016 to

spring 2017. U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office, Red

Bluff, California


Clear Creek Adult Rainbow Trout/steelhead and Late-fall run Chinook; winter 2016 to spring 2017 iii

Distribution and abundance of Rainbow Trout/steelhead and late-fall run

Chinook Salmon redds in Clear Creek; winter 2016 to spring 2017

Samuel S. Provins and Charles D. Chamberlain

U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office

10950 Tyler Road, Red Bluff, California 96080

Abstract — Clear Creek, a west-side tributary of the Sacramento River, provides spawning

habitat for both Rainbow Trout/steelhead Oncorhynchus mykiss and late-fall Chinook Salmon O.

tshawytscha. Since 2003 the United States Fish and Wildlife Service has completed spawning

surveys by kayak to quantify the amount of Rainbow Trout/steelhead and late-fall Chinook

spawning occurring in Clear Creek on an annual basis. In the 2016–2017 season, biologists

completed six surveys of Clear Creek from Whiskeytown Dam to the mouth. Survey crews

identified 75 Rainbow Trout/steelhead and 20 late-fall Chinook redds between December 6,

2016, and April 4, 2017. In the same period, data were collected from 13 late-fall Chinook

carcasses. Water year 2017 was one of the wettest in recent history for the California Central

Valley; many large storms influenced our ability to survey and collect information.


Clear Creek Adult Rainbow Trout/steelhead and Late-fall run Chinook; winter 2016 to spring 2017 iv

Table of Contents

Abstract ........................................................................................................................................................ iii

Table of Contents ......................................................................................................................................... iv

List of Tables ................................................................................................................................................ v

List of Figures ............................................................................................................................................... v

Introduction ................................................................................................................................................... 1

Study Area .................................................................................................................................................... 1

Methods ........................................................................................................................................................ 2

Redd Identification .................................................................................................................................... 2

Redd Measurements .................................................................................................................................. 3

Live Adults and Carcasses ........................................................................................................................ 3

Discharge, Temperature, and Turbidity Measurements ............................................................................ 3

Results ........................................................................................................................................................... 4

Redd Identification .................................................................................................................................... 4

Redd Measurements .................................................................................................................................. 4

Live Adults and Carcasses ........................................................................................................................ 5

Discharge, Temperature, and Turbidity Measurements ............................................................................ 5

Discussion ..................................................................................................................................................... 6

Acknowledgements ....................................................................................................................................... 7

References ..................................................................................................................................................... 8

Tables ............................................................................................................................................................ 9

Figures ........................................................................................................................................................ 12


Clear Creek Adult Rainbow Trout/steelhead and Late-fall run Chinook; winter 2016 to spring 2017 v

List of Tables

Table 1. The number of late-fall run Chinook Salmon and Rainbow Trout/steelhead redds,

carcasses and live adult observations summarized by survey. ..................................................... 10

Table 2. Date observed and samples collected from late-fall run Chinook Salmon (CHN) ......... 11

List of Figures

Figure 1. Map of study area in lower Clear Creek. ....................................................................... 13

Figure 2. Survey spatial and temporal coverage. .......................................................................... 14

Figure 3. Clear Creek Rainbow Trout/steelhead redds by date and river mile. ............................ 15

Figure 4. Clear Creek late-fall run Chinook Salmon redds by date and river mile. ..................... 16

Figure 5. Late-fall run Chinook Salmon and Rainbow Trout/steelhead redd area. ...................... 17

Figure 6. Length and width measurements of late-fall run Chinook Salmon and Rainbow

Trout/steelhead redds. ................................................................................................................... 18

Figure 7. Depth and velocity measurements at 30 Rainbow Trout/steelhead redds (40% of total

observed Rainbow Trout/steelhead redds). ................................................................................... 19

Figure 8. Depth and velocity measurements at five late-fall run Chinook Salmon redds (25% of

total observed late-fall run Chinook Salmon redds). .................................................................... 20

Figure 9. Dominant sediment size at Rainbow Trout/steelhead redds. ......................................... 21

Figure 10. Dominant sediment size at late-fall run Chinook Salmon redds. ................................ 22

Figure 11. Temperature (°F) and stream discharge (cfs) at IGO gaging station USGS (11372000).

....................................................................................................................................................... 23


Clear Creek Adult Rainbow Trout/steelhead and Late-fall run Chinook; winter 2016 to spring 2017 1

Introduction

The National Marine Fisheries Service (NMFS) listed California Central Valley steelhead

Oncorhynchus mykiss as a threatened species in 1998 under the Federal Endangered Species Act

(63 CFR § 13347). Their threatened status was reaffirmed following a five-year review in 2011

(NMFS 2011). In this report O. mykiss refers to both stream resident (Rainbow Trout) and

anadromous (steelhead) life histories because of the difficulties differentiating resident and

anadromous forms in the field. Central Valley late-fall run Chinook Salmon O. tshawytscha

(late-fall Chinook) were identified as a species of concern in 1999 (NMFS 2009).

Since 1995 the Central Valley Project Improvement Act, Clear Creek Fish Restoration

Program, and later the California Ecosystem Restoration Program have taken several restoration

actions to improve anadromous salmonid habitat in Clear Creek (California Department of Fish

and Wildlife et al. 2014; Bureau of Reclamation [BOR] and U.S Fish and Wildlife Service

[USFWS] 2016). Restoration actions have included increased minimum instream flows,

spawning gravel supplementation, dam removal, water temperature control through flow

management, and large-scale stream channel and floodplain restoration (BOR and USFWS

2016).

The Red Bluff Fish and Wildlife Office has conducted kayak based surveys since 2003 to

assess the abundance and distribution of adult O. mykiss and late-fall Chinook on Clear Creek,

and evaluate effects of restoration actions on their recovery. On Clear Creek, kayak surveys are

an effective method to obtain redd counts and carcasses during the spawning season when flows

are high and fluctuating due to storm events. This annual report summarizes monitoring efforts

for the 2016–2017 survey season.

Study Area

Lower Clear Creek extends from Whiskeytown Dam, river mile (RM) 18.3, and joins the

Sacramento River in south Redding, CA (Figure 1) at Sacramento RM 289. Lower Clear Creek

provides many habitat types due to spatial variation in stream gradient, catchment size, and

sediment supply. In dry periods discharge and water temperature are very sensitive to releases

from Whiskeytown Lake. In warmer months (when air temperature is greater than water

temperature) water warms as it flows downstream; in cooler months this trend is reversed and

water cools as it flows downstream. During storm events stream discharge increases into the

lower reaches as additional sources are accreted. Additionally, Clear Creek changes in

geomorphic character along its path from Whiskeytown Dam to the Sacramento River. McBain

and Trush (2001) summarized the settings found in Clear Creek by categorizing them into four

major reaches based on geomorphological attributes. The upstream most reach extends from

Whiskeytown Dam to Need Camp Bridge (RM 18.3–16.1) and is primarily characterized by an

unconfined alluvial stream type. The second reach, from Need Camp Bridge to the Clear Creek

Road Bridge (RM 16.1–8.6), is primarily composed of confined bedrock channels. The Saeltzer

Dam Reach extends from the Clear Creek Road Bridge through the Gorge Cascade (RM 8.6–

6.5), and it is characterized by a lower stream gradient and increasing alluvial nature. The

downstream most reach extends from the Gorge Cascade to the confluence with the Sacramento

River (RM 6.5–0) and has an unconfined alluvial morphology.



Methods

The primary objective of this annual survey is to detect and enumerate O. mykiss and

late-fall Chinook redds on Clear Creek. Additional objectives included collecting data on size

and location of these redds, documenting live late-fall Chinook fish observations, and collecting

spawning information and tissue samples from fish carcasses. In order to achieve these

objectives during the 2017 season, surveys were scheduled every other week from December

2016 through March 2017 to cover the historic spawning period for these species in Clear Creek.

Environmental conditions can occasionally degrade the quality of the data collected. Storm

events, high instream flow, and turbidity can make it difficult or dangerous to effectively survey.

Over time redds flatten and become difficult to detect; increases in discharge can hasten this

flattening thereby degrading some redds completely in a short period. Efforts were made in

scheduling surveys to balance these data risks and collect a robust dataset.

Five logistic reaches of Clear Creek were surveyed. These reaches averaged three river

miles in length and each took one day each to sample. An upper gorge reach (RM 11.0–13.2)

was omitted due to safety concerns posed by rapids and historically low redd densities

(Giovannetti et al. 2013). The most downstream reach ended at the Clear Creek video counting

weir (RM 0.1).

O. mykiss and late-fall Chinook redd surveys were completed by employing inflatable

kayaks for transit. On each survey day, three or four fish biologists kayaked from upstream to

downstream in a selected reach. Surveyors were each assigned a side of the creek to examine for

redds, live adult late-fall Chinook, and carcasses. When a crewmember identified a suspected

salmonid redd, adult live late-fall Chinook salmon, or carcass the survey team stopped to

investigate further as a group.

Redd Identification

As the surveyors kayaked downstream, clean gravel patches and areas of mounded and

sorted gravel indicated potential redd building activity. Following this initial observation, crew

members would assess if substrate at the location had two primary characteristics of a salmonid

redd: a pit and a tail-spill. The pit of a redd is the area of deposited substrate downstream of the

area excavated by the female salmonid in preparation and covering of fertilized eggs. The tail-

spill is downstream of the pit and is composed of the sediment that was displaced from the pit. A

pit and tail-spill can positively indicate a redd; however, considerable experience and training of

fish biologists is critical for the repeatable identification of salmonid redds and differentiation

from hydraulic scour features that can sometimes exhibit a similar appearance (Gallagher and

Gallagher 2005). Following a discussion of these traits and even closer examination of the redd

by snorkel and mask if needed, the crew collectively determined if the disturbance would be

recorded as a redd or not.

Spawning Chinook females are generally larger than spawning O. mykiss females. With

their larger body mass, Chinook are capable of excavating larger substrate sizes and typically

construct larger redds than O. mykiss. Each redd was attributed to either O. mykiss or late-fall

Chinook based on its overall size and the size of substrate moved in its construction. Locations

of substrate disturbance that may have been created by an adult female but lacked an identifiable

pit and tail were marked as test digging and checked on subsequent surveys. After a redd was

confirmed by crew consensus and attributed to a species, a biodegradable flag was hung at eye

level on vegetation even with the upstream extent of the redd. The GPS position of the pit of

each redd was recorded by handheld GPS. On subsequent surveys previously identified redds



were revisited and assessed for visibility to track how long they remained identifiable. These

visibility data are used in some years to inform the likelihood of missing redds constructed

between visits.

Redd Measurements

Measurements were taken on identified redds to characterize the habitat in which they

were built and their susceptibility to scour and dewatering. For each identified redd, biologists

assessed the source of substrate (supplementation gravel, native gravel, or combination). The

most prevalent size class of gravel was visually estimated in three locations around each redd:

(1) just upstream of the redd (pre-redd), (2) to the side of the pit (side-redd), and (3) in the tail-

spill.

For the first redd and every subsequent fifth redd of each species, additional

measurements were taken to describe the size, depth, and water velocity at the redd location. The

first two measurements taken were length and width of the redd. Length measurements were

taken at the longest straight line of spawning disturbance from upstream to downstream. Width

measurements were taken at the longest straight line of disturbance roughly perpendicular to the

flow. In order to calculate the area of a given redd the assumption and equation of an elliptical

shape was used (area = π· ½ L ·½ W). A depth measurement was taken at an estimated average

location within the pre-redd, at the greatest depth of the pit, and at the shallowest point of the tail

spill. Water velocity at the pre-redd location was measured at the depth representing mean water

column velocity with a mechanical flowmeter over a 100 second interval. Differences in redd

measurements between species were tested for significance by a Welch’s two-sample t-test.

Live Adults and Carcasses

In addition to locating salmonid redds, crew members observed and recorded live

Chinook adults and late-fall Chinook and O. mykiss carcasses. When live Chinook were

observed, the survey crew would proceed to the end of the habitat unit enumerating all live

Chinook encountered in the unit and store the location in a handheld GPS device. Also the

number of fish counted, any observed characteristics (sex, tail wear, ripeness, etc.), and external

tags (Floy) were reported. When an O. mykiss or late-fall Chinook carcass was spotted several

pieces of information and samples were gathered. Data collected included the species, sex, and

FL. Tissue samples were collected for genetic analysis along with scales and otoliths for later

analyses. If the adipose fin was either absent or could not be determined (i.e. carcass with a head

only) the head of the fish was returned to the office for Coded Wire Tag detection, extraction,

and evaluation. Finally, a photo was taken of each carcass observed.

Discharge, Temperature, and Turbidity Measurements

Discharge and water temperature in Clear Creek were measured at RM 11.1 at USGS

gage (11372000) in 30-minute intervals. Water temperature was also measured by loggers along

the length of Clear Creek from Whiskeytown Dam to the mouth at roughly two-river-mile-long

intervals. These data were summarized by calculating daily mean discharge and temperature for

each day in survey period. Turbidity was assessed by collecting a water sample at the beginning

and end of each field day of the survey for measurement with a turbidimeter back at office.



Results

Between December 2016 and April 2017 six surveys of spawning O. mykiss and late-fall

Chinook were completed on Clear Creek (Table 1, Figure 2).

Redd Identification

Surveyors identified 75 O. mykiss and 20 late-fall Chinook redds in the 2016-2017 survey

season (Table 1). The majority of the O. mykiss redds (73%) were identified in the lower alluvial

reach between the Gorge Cascade (RM 6.5) and the lower extent of our survey. Twenty-five

percent of the total O. mykiss redds were located in the upper alluvial reach between

Whiskeytown Dam (RM 18.1) and the Need Camp Bridge (RM 16.2). The remaining O. mykiss

redds (2%) were identified in the 9.7 river miles between these two alluvial reaches. Notably,

over 30% of O. mykiss redds were detected in a half-mile stretch of habitat within the lower

alluvial reach referred to as Renshaw Riffle (RM 5.1–5.6). The majority of O. mykiss redds

(57%) were detected on the first and second surveys of the season (18 and 25 redds,

respectively). Fewer redds were detected later in the season with the fewest redds (two) being

observed on the final survey (Figure 3).

All 20 late-fall Chinook redds were identified in the lower alluvial reach between the

Gorge Cascade (RM 6.5) and the video passage weir (RM 0.1). Four late-fall Chinook redds

(24%) were detected in a half mile stretch of habitat referred to as Renshaw Riffle (RM 5.6–5.1).

All but one late-fall Chinook redd were identified on either the first or the fifth survey (Figure 4).

Identifiable redd features degraded quickly for some redds and persisted longer for

others. Previously identified O. mykiss redds were assessed on subsequent surveys and found to

lose discernable features after 23 days on average (standard deviation = 10 days, n assessments =

5). Of the 49 redds assessed a second time 74% were not visible even under close inspection of

the area. Redds that were visible at the second assessment were generally both upstream of all

major tributary inputs and surveyed at a shorter time interval.

Redd Measurements

Additional measurements were taken on five late-fall Chinook redds and 30 O. mykiss

redds. The average area of redds identified as late-fall Chinook was 176 ft2. O. mykiss redds

averaged 17 ft2 in area. The largest redd classified as O. mykiss (74 ft2) was larger than the

smallest classified late-fall Chinook redd (33 ft2) (Figure 5). There was no interspecies overlap in

lengths and widths of redds; all length and width measurements for redds attributed to Chinook

were greater than those for O. mykiss (Figure 6). Both O. mykiss and late-fall Chinook redds

exhibited the expected relationship between depth measured at the pre-redd, pit, and tail-spill

with the depth of the pit being the greatest and the depth of the tail spill being the least (Figure 8,

Figure 8). A Welch’s two sample t-test confirmed that the means of pre-redd, pit and tail-spill

depth measurements were distinct for O. mykiss redds (P < 0.05) (e.g. the estimated mean depth

of an O. mykiss pre-redd is statistically distinct from the estimated mean depth of an O. mykiss

tail spill). The same test performed on late-fall Chinook redd measurements confirmed that the

estimated means of all three redd measurements were distinct (P < 0.05). Redds attributed to O.

mykiss and late-fall Chinook had statistically similar depths in the pre-redd (µO. mykiss = 13 in, µlate-fall

Chinook = 14.6 in; P = 0.63 ) and tail-spill (µO. mykiss = 11 in, µlate-fall Chinook = 8 in; P = 0.22), but slightly

more distinct pit depths (µO. mykiss = 17 in, µlate-fall Chinook = 20.8 in; P = 0.04).

Median, maximum, and minimum velocity measurements taken at O. mykiss redds (1.7

ft/s, 3.1 ft/s, and 0.92 ft/s, respectively; n = 29) were similar to the same metrics for



measurements at Chinook redds (2.1 ft/s, 2.9 ft/s, and 0.6 ft/s, respectively; n = 5) (Figure 7,

Figure 8). A Welch’s two-sample t-test comparing the velocity measurements from O. mykiss

and late-fall Chinook redds failed to detect a significant difference in the estimated mean of these

measurements (P = 0.98).

Substrate composition was visually assessed on all identified O. mykiss and late-fall

Chinook redds. In general, gravel in which late-fall Chinook built redds (and of which redds

were constructed) was larger than gravel used by O. mykiss. The dominant size class of gravel

identified in the pre-redd, side-redd, and tail-spill for O. mykiss was 1–2 inches; for late-fall

Chinook redds the dominant size class in the same areas was 1–3 inches (Figure 10, Figure 10).

Of the 75 O. mykiss classified redds, one was built in substrate without apparent influence

from gravel supplementation efforts. None of the observed late-fall Chinook redds were built in

substrate without apparent influence from gravel supplementation efforts.

Live Adults and Carcasses

Eighty-five adult late-fall Chinook were observed over the study period; all of these fish

were observed in the lower alluvial reach below the Gorge Cascade (RM 6.5). The majority

(98%) of observations occurred before February 1, 2017. The greatest number of live adult late-

fall Chinook observations occurred on the second survey of the year (Table 1).

Thirteen late-fall Chinook carcasses were identified and evaluated; all of these fish were

observed in the lower alluvial reach below the Gorge Cascade (RM 6.5). No O. mykiss carcasses

were observed in the 2016–2017 season. Of the 13 late-fall Chinook carcasses, two had a

positively identifiable adipose fin clip, 10 had an intact adipose fin, and adipose status was

unknown for one fish. Coded wire tags were present in both fish without adipose fins. These fish

were identified as brood year 2013 Fall Chinook. One fish was reared in the Feather River Fish

Hatchery and released at Half Moon Bay. The other was reared at the Mokulumne River Fish

Hatchery and released in the San Francisco Bay (Table 2).

Discharge, Temperature, and Turbidity Measurements

For the 2016–2017 season the average discharge at Igo during active surveying was 323

cubic feet per second (cfs). Over the entire survey season, mean daily discharge exceeded 1,000

cfs during five rain events and for fifteen individual days (Figure 11). The average water

temperature during active surveying was 47.2 °F. As measured at the Igo gage (RM 11.1), stream

temperature was warmer at the beginning and end of our survey season (roughly 52 °F on the

first and last surveys). Water temperature tended to rise during rain events (Figure 11). The

average turbidity over active surveying was 2.6 nephelometric turbidity units. The greatest

turbidity measurement on an individual survey was 5.58 nephelometric turbidity units; turbidity

was higher following storm events (Table 1).



Discussion

Spawning surveys have long been a fundamental method for assessing the population and

distribution of anadromous fishes. Other modern fisheries methods, such as ocean stock

assessments, video weir estimates of adult spawning fish entering an area or rotary screw trap

estimates of juvenile fish leaving an area, all provide abundance information. Each of these

methods probe at life-stage specific questions. Each has inherent method error and is subject to

additional potential error from environmental conditions (e.g. storms that reduce effectiveness or

survey effort). One strength of a diverse multi-method assessment of a population is that when

environmental factors lead to untenable estimation from a particular method, other methods of

abundance estimation may partially compensate. A robust assessment program should include

evaluation of both method and seasonal error.

The spawn timing of O. mykiss and late-fall Chinook in the Central Valley corresponds

with the rainy season in this region, and weather can introduce error in spawning monitoring by

making survey conditions difficult in Clear Creek. Increases in discharge can both scour redds

and degrade survey conditions. In previous seasons events, redd scour has been observed on

Clear Creek starting near 1,000 cfs (Sarah Gallagher USFWS, personal communication), though

Pittman and Mathews (2009) characterize bed mobilization events under 2,000 cfs as outliers.

Increases in discharge can also lead to higher water turbidity and error through decreased

visibility. In the 2016-2017 season, mean daily discharge frequently exceeded 1,000 cfs and

turbidity often influenced our surveyors’ ability to observe substrate. It is very likely that scour

or turbidity from discharge events introduced additional error in the redd, live adult or carcass

counts.

Often we can learn about how quickly redds flatten and scour from subsequent

observations of previously identified redds. This information is used to think about survey error

introduced by survey timing and storms. This year the majority of redds we mapped were not

visible on the subsequent survey, providing us with very little information about persistence of

identifiable characteristics. The extended period between surveys likely resulted in

underestimation of the number of redd constructed. Particularly in wet years, it could be valuable

to make additional observations and measurements on redds. Artificial redds near easily

accessible points could be used.

An assumption of this survey is that larger redds are constructed by late-fall Chinook.

Both coded wire tags extracted this season were not late-fall Chinook, but rather fall Chinook

Salmon, each from a different hatchery, and each part of an off-site release whereby they were

trucked to the San Francisco Bay area in 2014. With less than 100% mark rates of fall Chinook

from those hatcheries, it is possible that fall Chinook hatchery strays influenced portion of the

spawning attributed to late-fall Chinook in this survey.

Overall, environmental conditions this season made a robust survey schedule impossible.

Better quantification of spawning density and survey error would allow a model to estimate

survey error more proficiently.



Acknowledgements

We gratefully acknowledge the hard work and dedication of our kayak survey field crew,

Ryan Cook, RJ Bottaro, George Davis, Sarah Gallagher, Ryan Mckim, Sam Provins, Cameron

Reyes, Ryan Schaefer, Charles Stanley, Alan Webster and Travis Webster. We thank the

Whiskeytown National Recreation Area and the Bureau of Land Management for providing

creek access on public lands. We thank the Bureau of Reclamation for the continued support in

funding this project. Additionally, we thank RJ Bottaro, Charles Stanley and Mike Schraml for

providing edits and feedback on this report.



References

[BOR and USFWS] Bureau of Reclamation, U S Fish and Wildlife Service. 2016. Central Valley

Project Improvement Act Public Law 102–575, Annual Report, Fiscal Year 2014.

California Department of Fish and Wildlife, U.S. Fish and Wildlife Service, and National Marine

Fisheries Service. 2014. Ecosystem Restoration Program Conservation Strategy for

Restoration of the Sacramento san Joaquin delta, Sacramento Valley and San Joaquin Valley

Regions. Sacramento, CA.

Gallagher, S. P., and C. M. Gallagher. 2005. Discrimination of chinook salmon, coho salmon,

and steelhead redds and evaluation of the use of redd data for estimating escapement in

several unregulated streams in northern California. North American Journal of Fisheries

Management 25(1):284–300.

Giovannetti, S. L., RJ Bottaro, and M. R. Brown. 2013. Adult steelhead and late-fall Chinook

salmon Monitoring on Clear Creek, California: 2011 Annual report. U.S. Fish and Wildlife

Service, Red Bluff Fish and Wildlife Office, Red Bluff, California.

McBain and Trush. 2001. Final report: Geomorphic evaluation of lower Clear Creek downstream

of Whiskeytown Dam, California.

[NMFS] National Marine Fisheries Service. Endangered and Threatened Species: Threatened

Status for Two ESUs of Steelhead in Washington, Oregon, and California. 63 CFR § 13347

(03/19/1998)

National Marine Fisheries Service. 2009. Species of Concern: Chinook Salmon Central Valley

Fall , Late-fall run ESU.

http://www.westcoast.fisheries.noaa.gov/publications/SOC/chinooksalmon_detailed.pdf

National Marine Fisheries Service. 2011. 5-Year Review: Summary and Evaluation of Central

Valley Steelhead. U.S. Department of Commerce, 34 pp.

Pittman, S., and G. Matthews. 2009. Clear Creek gravel injection monitoring 2007–2009.

http://www.westcoast.fisheries.noaa.gov/publications/SOC/chinooksalmon_detailed.pdf



Tables



Table 1. The number of late-fall run Chinook Salmon and Rainbow Trout/steelhead redds, carcasses and live adult observations

summarized by survey. Environmental conditions collected during each survey week including average turbidity (NTU), water

temperature (°F), and discharge (cfs).

Late-fall run

Chinook Salmon

Rainbow

Trout/steelhead Environmental conditions

Survey

Middle

date Redds Carcass Live Redds Carcass

Average

turbidity

(NTU)

Average

water

temperature

(°F)

Average

discharge

(cfs)

1 12/7/2016 9 6 15 18 0 1.0 49.6 277

2 12/28/2016 1 1 35 25 0 2.0 45.2 315

3 1/17/2017 0 0 21 5 0 4.9 45.0 373

4 1/31/2017 0 1 12 16 0 3.6 45.7 359

5 3/16/2017 10 5 2 9 0 3.0 48.9 304

6 4/4/2017 0 0 0 2 0 2.4 51.4 345

Total 20 13 85 75 0



Table 2. Date observed and samples collected from late-fall run Chinook Salmon (CHN) The sex of each carcass is recorded as male,

female or unknown (M, F, U). Intact adipose fin indicated by a “1”, clipped by a “0”, unknown by “U”. For hatchery marked fish that

a coded wire tag was recovered from, hatchery origin information is listed. All carcasses listed were identified during kayak surveys.

Biological sample Coded wire tag information

Survey Date

River

mile Sex Adipose

FL

(mm) Genetics Scale Otolith

Tag

code

Run Brood

year

Hatchery

1 12/7/2016 5.8 F 0 750 1 1 1 060618 Fall 2013 Feather

1 12/7/2016 4.3 F 1 800 1 1 1

1 12/7/2016 3.6 M 0 825 1 1 1 060570 Fall 2013 Mokelumne

1 12/7/2016 1.5 M 1 850 1 1 1

1 12/7/2016 1.4 F 1 610 1 1 1

1 12/7/2016 1.0 F 1 670 1 1 1

2 12/28/2016 1.6 U 1 0 0 0

4 1/31/2017 3.2 U U 1 1 0

5 3/14/2017 2.3 M 1 0 0 0

5 3/14/2017 2.1 M 1 1020 1 1 1

5 3/14/2017 0.6 M 1 0 0 0

5 3/14/2017 4.0 M 1 950 1 1 1

5 3/14/2017 2.8 M 1 1 1 1



Figures



Figure 1. Map of study area in lower Clear Creek. The survey included the stream between

Whiskeytown Dam and the Sacramento River, excluding the areas noted in the map. From

upstream to downstream, the major geomorphic habitat sections found in Clear Creek are:

unconfined alluvial channel (through river mile 16.1), confined bedrock channel (through river

mile 8.6), reach of lower gradient and increasing alluvial nature (through river mile 6.5) and an

unconfined alluvial channel through the confluence with the Sacramento River.



Figure 2. Survey spatial and temporal coverage.Dashed lines indicate the timing and spatial

extent of kayak surveys in the 2016-2017 survey season. Dark blue lines indicate days when the

mean daily flow on Clear Creek exceeded 1000 cfs. Redds created in the areas shaded blue may

have been obscured by discharge impacts. Black areas indicate the stream areas that were not

surveyed in the following 33 days. Redds created in the area shaded black may have been

obscured by redd flattening or other timing impacts. Previous redd ageing data was used to

calculate that at flows near 200 cfs. Greater than 95 percent of redds last longer than 33 days

(Provins and Chamberlain 2019). White areas indicate creek areas where we can be confident

that redds, if encountered were visible to a survey crew.



Figure 3. Clear Creek Rainbow Trout/steelhead redds by date and river mile. Each marker is an

individual Rainbow Trout/steelhead redd observed during the 2016–2017 survey season. The x-

axis indicates the initial survey date at which the redd was first observed. The left y-axis is the

river mile on Clear Creek. The red line displays the cumulative proportion of redds to date scaled

to the right y-axis.



Figure 4. Clear Creek late-fall run Chinook Salmon redds by date and river mile. Each marker is

an individual late-fall Chinook redd observed during the 2016–2017 survey season. The x-axis

indicates the initial survey date at which the redd was first observed. The left y-axis is the river

mile on Clear Creek. The red line displays the cumulative proportion of redds to date scaled to

the right y-axis.



Figure 5. Late-fall run Chinook Salmon and Rainbow Trout/steelhead redd area. The bolded line

inside each box represents the median measurement. The “box” encloses the interquartile range

or the range of 25% of the measurements above and below the mean. The horizontal line above

and below each box represents the maximum and minimum measurements.



Figure 6. Length and width measurements of late-fall run Chinook Salmon and Rainbow

Trout/steelhead redds.



Figure 7. Depth and velocity measurements at 30 Rainbow Trout/steelhead redds (40% of total

observed Rainbow Trout/steelhead redds). Depths were measured at the pre-redd, pit and tail-

spill of each Rainbow Trout/steelhead redd. Velocity measurements were taken at the pre-redd.

The bolded line inside each box represents the median measurement. The “box” encloses the

interquartile range or the range of 25% of the measurements above and below the mean. The

horizontal line above and below each box represents the maximum and minimum measurements.



Figure 8. Depth and velocity measurements at five late-fall run Chinook Salmon redds (25% of

total observed late-fall run Chinook Salmon redds). Depth measurements taken at the pre-redd,

pit and tail-spill of each Chinook redd. Velocity measurements were taken at the pre-redd. n =

the number of redds measured. The bolded line inside each box represents the median

measurement. The “box” encloses the interquartile range or the range of 25% of the

measurements above and below the mean. The horizontal line above and below each box

represents the maximum and minimum measurements.



Figure 9. Dominant sediment size at Rainbow Trout/steelhead redds. Sediment size class was

visually assessed at the pre-redd, pit and tail spill of each Rainbow Trout/steelhead redd. The

stacked bar graphs display the proportion of redds with a certain size class as dominant, for each

area of the redd.



Figure 10. Dominant sediment size at late-fall run Chinook Salmon redds. Dominant sediment

size class was visually assessed at the pre-redd, pit and tail spill of each late-fall run Chinook

Salmon redd. The stacked bar graphs display the proportion of redds with a certain size class as

dominant, for each area of the redd.



Figure 11. Temperature (°F) and stream discharge (cfs) at IGO gaging station USGS (11372000).

Stream temperature measured at river mile 11.1 is represented by a red line and scaled by the

right y-axis. Stream discharge as measured at river mile 11.1 is represented by a blue line and

scaled by the left y-axis. Vertical dotted lines indicate survey days.

Documents

Distribution and Abundance of Rainbow Trout/Steelhead and ... BC/Clear Creek Monitoring Final Reports... · Clear Creek Adult Rainbow Trout/steelhead and Late-fall run Chinook; winter