LOS GATOS CREEK BRIDGE
REPLACEMENT / SOUTH TERMINAL
PHASE III PROJECT
NMFS and USFWS
Biological Assessment
Prepared for
Peninsula Corridor Joint Powers Board
1250 San Carlos Avenue
P.O. Box 3006
San Carlos, California 94070-1306
and the
Federal Transit Administration Region IX
U.S. Department of Transportation
201 Mission Street
Suite1650
San Francisco, CA 94105-1839
Prepared by
HDR Engineering, Inc.
2379 Gateway Oaks Drive
Suite 200
Sacramento, California 95833
August 2013
NMFS and USFWS
Biological Assessment
Prepared for
Peninsula Corridor Joint Powers Board
1250 San Carlos Avenue
P.O. Box 3006
San Carlos, California 94070-1306
and the
Federal Transit Administration Region IX
U.S. Department of Transportation
201 Mission Street
Suite 1650
San Francisco, CA 94105-1839
Prepared by
HDR Engineering, Inc.
2379 Gateway Oaks Drive, Suite 200
Sacramento, California 95833
August 2013
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Los Gatos Creek Bridge Replacement / South Terminal Phase III June 2013
NMFS and USFWS Biological Assessment Page i
Summary
The Peninsula Corridor Joint Powers Board (JPB) which operates the San Francisco Bay Area’s
Caltrain passenger rail service proposes to replace the two-track railroad bridge that crosses Los
Gatos Creek, in the City of San Jose, Santa Clara County, California. The Proposed Action is
needed to address the structural deficiencies and safety issues of the Caltrain Los Gatos Creek
railroad bridge to be consistent with the standards of safety and reliability required for public
transit, to ensure that the bridge will continue to safely carry commuter rail service well into the
future, and to improve operations at nearby San Jose Diridon Station and along the Caltrain rail
line.
This Biological Assessment (BA) has been prepared for the National Marine Fisheries Service
(NMFS) and U.S. Fish and Wildlife Service (USFWS) to ensure compliance with Section 7 of
the Federal Endangered Species Act (ESA) due to the potential for listed, proposed to be listed,
or candidate aquatic and terrestrial species and designated critical habitat under the jurisdiction
of NMFS and USFWS to occur in the Action Area. In addition, Essential Fish Habitat (EFH) for
various species managed under the Magnuson-Stevens Fishery Conservation and Management
Act (MSFCMA) has been designated within Los Gatos Creek; therefore consultation with NMFS
is required.
As discussed herein, the BA determines to what extent the Proposed Action may affect any of
the endangered and threatened species and EFH that may occur in the Action Area. Based on
existing conditions and characteristics of the Action Area, one aquatic species, one terrestrial
species, and one species within an EFH were evaluated for potential effects: Central California
Coast Steelhead Distinct Population Segment (NMFS jurisdiction), California Red-legged Frog
(USFWS jurisdiction), and Central Valley fall-run Chinook Salmon (managed under the Pacific
Coast Fisheries Management Plan (FMP); NMFS jurisdiction).
The BA concludes that the Proposed Action “is not likely to adversely affect” Central California
Coast steelhead and California Red-legged Frog, and will have “no effect” on critical habitat for
Central California Coast steelhead and California Red-legged Frog. Also, the Proposed Action is
“not likely to adversely affect” Central Valley fall-run Chinook Salmon managed under the
Pacific Coast Salmon FMP or their designated EFH.
Los Gatos Creek Bridge Replacement / South Terminal Phase III July 2013
NMFS and USFWS Biological Assessment Page ii
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Los Gatos Creek Bridge Replacement / South Terminal Phase III July 2013
NMFS and USFWS Biological Assessment Page iii
Table of Contents
Summary ....................................................................................................................................................... i
1.0 Introduction ................................................................................................................................. 1-1
1.1 Regulatory Framework ..................................................................................................... 1-1
1.2 Project Location ............................................................................................................... 1-3
1.3 Purpose and Need of Proposed Action............................................................................ 1-3
1.3.1 Existing Safety Concerns .................................................................................... 1-5
1.3.2 Need for a Tail Track .......................................................................................... 1-5
1.3.3 Purpose of the Proposed Project ........................................................................ 1-6
2.0 Description of the Proposed Action .......................................................................................... 2-1
2.1 Project Elements .............................................................................................................. 2-1
2.2 Construction Staging ........................................................................................................ 2-4
3.0 Action Area .................................................................................................................................. 3-1
3.1 Location of the Action Area .............................................................................................. 3-1
3.2 Existing Environment ....................................................................................................... 3-1
3.2.1 Hydrology and Water Quality .............................................................................. 3-1
3.2.2 Groundwater ....................................................................................................... 3-7
3.2.3 Stormwater .......................................................................................................... 3-8
3.2.4 Geology and Geomorphology ............................................................................. 3-8
3.2.5 Land Use ........................................................................................................... 3-10
3.2.6 Fish Habitat and Fish Community Description .................................................. 3-10
3.2.7 Terrestrial Habitat Types/Vegetation Communities .......................................... 3-11
3.2.8 Sensitive Natural Communities/Wetlands and Waters of the U.S. ................... 3-13
4.0 Species and Habitat Considered ............................................................................................... 4-1
4.1 Species Included in the Analysis ..................................................................................... 4-1
4.2 Species Eliminated from the Analysis .............................................................................. 4-1
4.3 Critical Habitat .................................................................................................................. 4-4
4.4 Essential Fish Habitat ...................................................................................................... 4-5
4.5 Consultation to Date......................................................................................................... 4-5
5.0 Species Accounts ....................................................................................................................... 5-1
5.1 Listed Aquatic Species ..................................................................................................... 5-1
5.1.1 Central California Coast Steelhead DPS ............................................................ 5-1
5.2 Listed Terrestrial Species ................................................................................................ 5-4
5.2.1 California Red-legged Frog ................................................................................. 5-4
6.0 Effects on Species and Habitat ................................................................................................. 6-1
Los Gatos Creek Bridge Replacement / South Terminal Phase III July 2013
NMFS and USFWS Biological Assessment Page iv
6.1 Listed Aquatic Species ..................................................................................................... 6-2
6.1.1 Central California Coast Steelhead DPS ............................................................ 6-3
6.2 Listed Terrestrial Species .............................................................................................. 6-12
6.2.1 California Red-Legged Frog .............................................................................. 6-12
6.3 Determination of Effects ................................................................................................. 6-15
7.0 Conservation Measures.............................................................................................................. 7-1
8.0 Essential Fish Habitat Assessment .......................................................................................... 8-1
8.1 Essential Fish Habitat Background ........
