Appendix K: 

Fish, Vegetation, and Wildlife

Discipline Report

Point Defiance Bypass 

Project

Fish, Wildlife, and 

Vegetation 

Discipline Report 

September 2012 

Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page i 

Table of Contents 

Summary ......................................................................................................................................................... 1

Chapter 1 – Project Description ...................................................................................................................... 3

Introduction.................................................................................................................................................. 3

Purpose and Need ...................................................................................................................................... 3

What alternatives are being considered for the Point Defiance Bypass Project? ........................................ 4

What’s happening in the bypass corridor today? ......................................................................................... 4

What would happen if the Project were not built? ........................................................................................ 5

What are the proposed improvements and related activities of the Point Defiance Bypass Project? .......... 5

What are the proposed operational changes that would result from the Point Defiance Bypass Project? ... 6

Chapter 2 –Methodology ................................................................................................................................. 8

What is the study area for the Project? ....................................................................................................... 8

How was information about fish, wildlife, and vegetation collected? ...........................................................8

Chapter 3 – Affected Environment ................................................................................................................ 11

Fish Habitat in the Study Area ................................................................................................................... 11

Fish Presence in the Study Area ............................................................................................................... 17

Wildlife Habitat in the Study Area .............................................................................................................. 19

Wildlife Presence in the Study Area .......................................................................................................... 19

Vegetation in the Study Area ..................................................................................................................... 21

Chapter 4 – Project Effects ........................................................................................................................... 24

Would fish, wildlife, or vegetation resources be impacted or affected? ..................................................... 24

Chapter 5 – Recommended Minimization Measures ..................................................................................... 26

What minimization is required for the No Build Alternative? ...................................................................... 26

What minimization is required for the Build Alternative? ........................................................................... 26

References .................................................................................................................................................... 29
September 2012 Point Defiance Bypass Project 

Page ii Fish, Wildlife, and Vegetation Discipline Report 

List of Exhibits 

Exhibit 1. Build Alternative Components ......................................................................................................... 7

Exhibit 2. Streams in the Study Area ............................................................................................................. 12

Exhibit 3. Federally Listed Fish Species of the Puget Sound Region ............................................................ 17

Exhibit 4. Fish Presence within the Study Area ............................................................................................. 18

Exhibit 5. Listed Wildlife Species and Critical Habitats in Pierce County ...................................................... 20

Exhibit 6. Wetlands in the Study Area ........................................................................................................... 23

Exhibit 7. Federal and State-Listed Plants in Pierce County ......................................................................... 23
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 1 

Summary 

This report has been prepared in support of the Point Defiance Bypass 

Project (the Project) Environmental Assessment ,and in accordance with 

the National Environmental Policy Act (40 CFR 1500-1508), the State 

Environmental Policy Act (WAC 197-11), and the Federal Railroad 

Administration’s Procedures for Considering Environmental Impacts (64 

Fed. Reg. 28550). 

The purpose of the Project is to provide more frequent high-speed intercity 

passenger rail service between Tacoma and Nisqually. By increasing rail 

capacity, the Project would support additional Amtrak service between 

Portland, Oregon, and Seattle, Washington. 

The Project is located in Pierce County along an approximately 21-mile 

railroad existing corridor,1

 which passes through portions of the cities of 

Tacoma, Lakewood, and DuPont. The northern limit of the Project is near 

the crossing of Interstate 5 (I-5) over the Puyallup River in Tacoma, while 

the southern limit of the Project is near the crossing of Nisqually Road 

over the Nisqually River. 

Due to the existing high disturbance baseline within this populated region, 

the study area is limited to those zones within a 200-foot radius of the 

railroad right-of-way, which incorporates both the construction footprint 

within the right-of-way and adjacent areas potentially exposed to visual 

disturbance and elevated noise during and after construction. 

Seven streams occur within the right-of-way, one (Clover Creek) of which 

is documented as supporting winter steelhead (FT)2

 and coho salmon 

(FSC).3 No in-water work is proposed, and Best Management Practices 

(BMPs) during construction would prevent effects to water quality. As a 

result, no effect to fish as a result of the Project is anticipated. 

Due to existing baseline disturbance from surrounding urban development, 

automobile and train traffic, human activity, and vegetation management, 

suitable habitat for wildlife listed under the Endangered Species Act 

(ESA) is absent within the study area. Therefore, no effect to ESA-listed 

wildlife as a result of the Project is anticipated. 

 

1

 The three owners of the proposed Project corridor are Sound Transit, Tacoma Rail, and BNSF. 2

 Federally listed as Threatened. 

3

 Federally listed as a Species of Concern. 
September 2012 Point Defiance Bypass Project 

Page 2 Fish, Wildlife, and Vegetation Discipline Report 

Vegetation disturbance would be limited to the railroad right-of-way 

where, due to railroad maintenance and operations, conditions are not 

suitable for plants listed under the ESA. Therefore, no effect to ESA-listed 

plants as a result of the Project is anticipated. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 3 

Chapter 1 – Project Description 

Introduction 

Under the High-Speed Intercity Passenger Rail (HSIPR) Program and 

pursuant to a programmatic Tier I Environmental Assessment (EA) the 

Federal Railroad Administration (FRA) has approved an application from 

the Washington State Department of Transportation (WSDOT) to improve 

the Pacific Northwest Rail Corridor (PNWRC), a federally designated 

high-speed rail corridor. One project included in the PNWRC application 

is the Point Defiance Bypass Project (the Project), which would respond to 

deficiencies in the existing rail operations around Point Defiance. This 

Discipline Report has been prepared in support of the project-specific EA 

for the Point Defiance Bypass project. 

The Project is located in Pierce County along an existing approximately 

20-mile rail corridor between Tacoma and Nisqually.4 The Project would 

provide for the re-routing of Amtrak passenger trains from the BNSF rail 

line that runs along the southern Puget Sound shoreline (Puget Sound 

route) to the Point Defiance Bypass route, an existing rail corridor that 

runs along the west side of I-5. The Project would consist of railroad track 

and support facility improvements, and relocation of the Tacoma Amtrak 

Station to Freighthouse Square in Tacoma. 

Purpose and Need

As described above, the Point Defiance Bypass route is part of the larger 

PNWRC. Within Washington State, the vision for the PNWRC is to 

“...improve intercity passenger rail service by reducing travel times and 

achieving greater schedule reliability in order to accommodate growing 

intercity travel demand...”5. 

The purpose of the Project is to provide more frequent and reliable highspeed intercity passenger rail service along the PNWRC between Tacoma 

and Nisqually. In conformity with the decisions under the Tier 1 

Programmatic EA, the PNWRC Improvement Program has reduced the 

overall environmental effects of providing improved passenger rail service 

with the use of an existing transportation corridor and associated 

infrastructure, rather than creating a new corridor. 

 

4

 The three owners of the project corridor are Sound Transit, Tacoma Rail, and BNSF. 5 WSDOT 2009
September 2012 Point Defiance Bypass Project 

Page 4 Fish, Wildlife, and Vegetation Discipline Report 

The Project is needed to address the deficiencies in the existing rail 

alignment around Point Defiance. The existing alignment (Puget Sound 

route), shared by freight and passenger rail traffic, is near capacity and is 

therefore unable to accommodate additional high-speed intercity 

passenger rail service without substantial improvements. In addition, the 

existing alignment has physical and operational constraints that adversely 

affect both passenger train scheduling and reliability. 

Improving intercity passenger rail service in the project area and meeting 

the Project needs would be accomplished by: 

 Enhanced Frequency: Increasing Amtrak Cascades round-trips from four 

to six by 2017 to meet projected service demands. 

 Improved Reliability: Reducing scheduling conflicts with freight trains 

that often result in delays, and by minimizing or avoiding operational 

delays (e.g., drawbridge openings) and weather-related delays (e.g., 

mudslides), and improving on-time performance from 68 percent to 88 

percent. 

 Enhanced Efficiency: Enhancing the efficient movement of people by 

decreasing trip times by 10 minutes, and reducing the amount of time 

passenger trains spend yielding to freight movements. 

 Improved Safety: Constructing at-grade crossings with upgraded safety 

features, including wayside horns, median barriers, advance warning 

signals, and traffic signal improvements. 

What alternatives are being considered for the Point 

Defiance Bypass Project? 

FRA and WSDOT conducted an evaluation of three build alternatives: the 

Point Defiance Bypass Alternative, the Shoreline Alternative, and the 

Greenfield Alternative. Two of the alternatives (the Shoreline Alternative, 

and the Greenfield Alternative) were eliminated from further study. 

Although both alternatives could meet the Project’s purpose and need, 

they were determined to be impracticable and unfeasible due to technical 

constraints, high construction costs, and significant environmental effects. 

Grade separations were also evaluated for further consideration. FRA and 

WSDOT’s preliminary analysis revealed that current and projected future 

traffic volumes do not warrant the construction of new grade-separated 

crossings. 

What’s happening in the bypass corridor today? 

The rail line between TR Junction and East “D” Street in Tacoma hosts 

both freight and commuter trains, including freight operators Tacoma Rail 

and BNSF, and Sound Transit’s Sounder commuter rail service. Freight 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 5 

train traffic between TR Junction and East “D” Street averages under two 

trains per day, while Sound Transit currently operates 18 trains per day 

between Freighthouse Square and Seattle each weekday, and also offers 

occasional special event trains, usually on weekends, to serve sporting and 

other events in Seattle. Sounder service to Lakewood begins in late 2012. 

What would happen if the Project were not built? 

If the Project were not built (the No Build Alternative), Amtrak’s 

Cascades and Coast Starlight passenger train service would continue to 

use the existing Puget Sound route. The No Build Alternative includes 

only the minor maintenance and repair activities necessary to keep the 

existing Puget Sound route operational. With the No Build Alternative, it 

would be expected that as freight traffic increases, congestion would 

adversely affect Amtrak service reliability, and the travel time for Amtrak 

trains between Seattle and Portland would increase. 

Along the Point Defiance Bypass route, the Tacoma Rail and BNSF 

freight services would continue. The at-grade crossings at Clover Creek 

Drive Southwest, North Thorne Lane Southwest, Berkeley Street 

Southwest, 41st Division Drive, and Barksdale Avenue Southwest would 

not be upgraded. 

Sound Transit’s Sounder commuter passenger trains will become 

operational in late 2012 between the Tacoma Dome Station at 

Freighthouse Square in Tacoma and Sound Transit’s Lakewood Station 

(on the Point Defiance Bypass route) with as many as 18 Sounder trains 

per day. 

What are the proposed improvements and related activities 

of the Point Defiance Bypass Project? 

The Project consists of railroad track and support facility improvements, 

and the relocation of Amtrak’s Tacoma Station. Exhibit 1 shows the 

components of the Build Alternative. The following details specific 

components of the Build Alternative. 

 Construct New Track Adjacent to the Existing Main Line – A new 

3.5-mile track adjacent to the existing main line would be constructed 

from South 66th Street (Rail MP 6.9) in Tacoma to between Bridgeport 

Way SW (Rail MP 10.4) and Clover Creek Drive SW (Rail MP 10.9) in 

Lakewood. 

 Reconstruct and Rehabilitate the Existing Main Line – Starting just 

southwest of Bridgeport Way Southwest (Rail MP 10.4) in Lakewood, the 

existing track would be reconstructed to a location southeast of the I-
September 2012 Point Defiance Bypass Project 

Page 6 Fish, Wildlife, and Vegetation Discipline Report 

5/Mounts Road Southwest interchange (Rail MP 19.8) at Nisqually 

Junction. 

 Improvements at at-Grade Crossings – Several grade crossings would 

be improved with wayside horns, gates, traffic signals and signage, 

sidewalks, median separators, and warning devices. These crossings 

include Clover Creek Drive Southwest, North Thorne Lane Southwest, 

Berkeley Street Southwest, 41st Division Drive and Barksdale Avenue. 

 Tacoma Amtrak Station Relocation – The existing Tacoma Amtrak 

Station would be relocated from its Puyallup Avenue location to the 

Tacoma Dome Station at Freighthouse Square, at 430 E. 25th Street in 

Tacoma. 

What are the proposed operational changes that would 

result from the Point Defiance Bypass Project? 

Amtrak’s existing Cascades and Coast Starlight passenger train service 

would be rerouted from the Puget Sound route along the Puget Sound 

shoreline to the Point Defiance Bypass route. The Project would also 

provide for additional Amtrak Cascades service by increasing the number 

of round trips provided from 4 to 6, or a total of 12 Cascades service train 

trips. Amtrak Coast Starlight would also travel on the Point Defiance 

Bypass route for a total of two Coast Starlight service train trips. The 

speed of these passenger trains would be up to 79 mph. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 7 

Exhibit 1. Build Alternative Components 
September 2012 Point Defiance Bypass Project 

Page 8 Fish, Wildlife, and Vegetation Discipline Report 

Chapter 2 –Methodology 

This section presents the methods used to analyze potential effects to fish, 

wildlife, and vegetation resulting from the construction of the Project. 

What is the study area for the Project? 

The northern limit of the Project is the TR Junction near the I-5 

overcrossing of the Puyallup River and East Bay Street in Tacoma 

(Exhibit 1).6

 The southern limit of the Project is at Nisqually, a junction 

that is also on the Point Defiance Bypass Route, about one-third of a mile 

due north of where Nisqually Road crosses the Nisqually River (Exhibit 

1).7

The Project passes through portions of the cities of Tacoma, Lakewood, 

and DuPont, federal military (Army) installations at Camp Murray and 

Joint Base Lewis McChord (JBLM), and portions of unincorporated Pierce 

County. I-5, local roads, and commercial zones lie adjacent to the railroad 

right-of-way along most of the Project’s length. Existing baseline 

disturbance of vegetation and habitat is correspondingly high, including 

automobile and train traffic, human activity, artificial light, commercial 

and residential development, stream encroachment, culverting and 

bridging of streams, and fragmentation of vegetation communities. Due to 

the high baseline disturbance level, the effects of construction and future 

increase in rail traffic (noise, visual disturbance) are expected to be 

discountable. 

Accordingly, the study area for the Project is limited to those areas within 

a 200-foot radius of the existing railroad right-of-way, a zone which 

incorporates both the construction footprint within the right-of-way as 

well as all areas within 200 feet that may be exposed to increased visual 

disturbance and noise during and after construction. 

How was information about fish, wildlife, and vegetation 

collected? 

In August 2007, a Fish, Wildlife, and Vegetation Technical Memorandum 

was prepared by HDR Engineering, Inc. (HDR 2007) for the Project that 

 

6

 The north end of the proposed Project is in Township 20N, Range 30E, Section 10. 7

 The south end of the proposed Project is in Township 18N Range, 10E, Section 39. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 9 

evaluated fish, wildlife, and vegetation resources within the railroad rightof-way, the limits of which spanned from approximately South 66th Street 

in Tacoma to the BNSF Main Line south of DuPont. 

HDR’s methodology to collect information on fish, wildlife, and 

vegetation included background research and site visits in November and 

December 2006, and in January 2007. Field investigations were limited to 

the railroad right-of-way, where accessible. Field surveys consisted of 

walking the right-of-way and documenting wildlife species and plant 

communities observed. For fisheries, documentation included visual 

inspection of potential habitat for threatened and endangered species and 

identification of fish passage barriers. 

Since 2007, the Project has been expanded to include additional rail within 

the city limits of Tacoma from approximately South 66th Street north to 

the crossing of I-5 over the Puyallup River. To incorporate this expansion, 

the current study area includes the right-of-way limits evaluated by HDR 

in 2007 as well as the new right-of-way segment added within the 

developed city limits of Tacoma and adjacent areas within 200 feet of the 

right-of-way. 

In order to verify data presented by HDR in its 2007 Technical 

Memorandum for incorporation into this report, two field visits were 

conducted by qualified professionals on March 10, 2011, and April 14, 

2011. In March, the Project right-of-way and adjacent areas were observed 

by automobile in order to evaluate the Project within the context of 

surrounding development and disturbance. In April, a Hi-rail vehicle was 

driven upon the existing rail in order to observe all areas within the 

railroad right-of-way and adjacent areas. Where a closer inspection was 

warranted for verification purposes, the right-of-way was walked. Weather 

conditions during both visits were typical for the time of year and 

favorable for conducting field surveys. 

Based on the field information collected, it was determined that data 

presented by HDR in its 2007 Fish, Wildlife, and Vegetation Technical 

Memorandum are still accurate in describing applicable fish, wildlife, and 

vegetation resources within the right-of-way and that no new fish, wildlife, 

and vegetation resources are present within the current (expanded) study 

area. 

Therefore, the information presented in this report is, in large part, derived 

from HDR (2007), with updates incorporated where relevant. 

Background Research 

The following data sources were reviewed to determine the potential for 

fish, wildlife, and vegetation resources to occur in the study area: 
September 2012 Point Defiance Bypass Project 

Page 10 Fish, Wildlife, and Vegetation Discipline Report 

 US Fish and Wildlife Service (USFWS) – Endangered Species 

Act-listed (ESA-listed) species database for Pierce County 

 Washington State Department of Wildlife (WDFW) Species of 

Concern List 

 WDFW Priority Habitats and Species (PHS) geospatial database 

 JBLM military installation – digital GIS data on natural resources 

 Washington State Department of Natural Resources (WDNR) 

Natural Heritage Program (NHP) – data on rare plant species 

 National Oceanic and Atmospheric Administration Fisheries 

(NOAA Fisheries) – ESA status of West Coast salmon and 

steelhead 

 Salmon and Steelhead Stock Inventory – occurrence of threatened, 

endangered, and sensitive fish species 

 SalmonScape database – digital GIS data on fish presence 

 StreamNet – resident fish presence 

 National Bald Eagle Management Guidelines 

 WDFW Bald Eagle Territory History 

 Pierce County Noxious Weed List 

 Literature on fish life history and distribution 

 Aerial photography. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 11 

Chapter 3 – Affected Environment 

This section describes the existing habitat conditions within the study area 

and evaluates the potential for fish, wildlife, and vegetation to be present. 

Fish Habitat in the Study Area 

The Project is located in three Water Resources Inventory Areas (WRIAs): 

Puyallup-White (WRIA 10); Chambers-Clover (WRIA 12); and Nisqually 

(WRIA 11). The Project also occurs within three 6th-field Hydrologic Unit 

Codes (HUCs): Chambers Creek (171100190303); Sequalitchew CreekFrontal Cormorant Passage (171100190304); and Nisqually River-Frontal 

Puget Sound (171100150307). 

Seven streams were identified in the study area (see Exhibit 2). From 

north to south, they are: First Creek; Tacoma Eastern Gulch; Stream 1 

(Unnamed Tributary to Flett Creek); Clover Creek; Stream 2 (Unnamed 

Tributary to American Lake); Murray Creek; and Stream 3 (Unnamed 

Tributary to the Nisqually River). These streams are described in detail 

below. 
September 2012 Point Defiance Bypass Project 

Page 12 Fish, Wildlife, and Vegetation Discipline Report 

Exhibit 2. Streams in the Study Area 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 13 

First Creek 

The Project would cross First Creek near Rail MP 0.85. The First Creek 

Watershed collects runoff from approximately 2,680 acres and conveys it 

through two tributary channels and a main stream channel, which are each 

located in 20- to 30-foot deep ravines. This stream network is managed by 

the City of Tacoma as a stormwater conveyance system and utility 

corridor. It has undergone historical maintenance for erosion, including 

the placement of rip rap into the channels. South of the Project boundary 

at E. 34th Street, First Creek enters a 6-foot-diameter pipe that conveys the 

stream under I-5 and the existing rail corridor, and then discharges to the 

Puyallup River approximately 630 feet downstream of I-5.8 First Creek 

supports fish, although anadromous salmonids are not known to use this 

stream. 

Tacoma Eastern Gulch 

The Project would cross a constructed watercourse called the Tacoma 

Eastern Gulch, also referred to as the “A” Street gully, at Rail MP 2.15. 

This watercourse flows under the Project corridor through a 6-footdiameter culvert before discharging into the Thea Foss Waterway.9

 No 

natural or critical area habitat is associated with the Tacoma Eastern 

Gulch. Fish are not known to occur in this stream. 

The Thea Foss Waterway sub-basin covers approximately 5,780 acres in 

south-central Tacoma. This sub-basin is mostly residential, with some 

commercial and industrial land use.10 

The Thea Foss Waterway is a current Superfund sediment cleanup site and 

is identified on Ecology’s 303(d) list for exceedance of polychlorinated 

biphenyls (PCBs) in tissue samples.11

Stream 1 (Unnamed Tributary to Flett Creek) 

Stream 1 drains an urban area to the southeast of South Tacoma Way and 

South 74th Street in which residential and commercial development is 

interspersed with vegetated open space. The stream is confined to a 

narrow, densely vegetated ditch that runs between large, paved parking 

lots before it is directed through long culverts under South Tacoma Way 

and the railroad embankment. The stream enters the Flett Creek Holding 

Basin west of the railroad. No fish are documented in Stream 1. 

 

8 Tacoma 2011a. 

9 Federal Transit Administration 2002. 

10 Tacoma 2011b. 

11 Ecology 2009. 
September 2012 Point Defiance Bypass Project 

Page 14 Fish, Wildlife, and Vegetation Discipline Report 

Clover Creek 

The contributing basin for Clover Creek largely occurs east of JBLM, a 

region interspersed with residential development, commercial zones, and 

golf courses. Water flows toward the west as it is culverted 2,500 feet 

under the AFB runway, I-5, and railroad before it enters Steilacoom Lake. 

The creek leaves Steilacoom Lake as Chambers Creek, which flows 2.5 

miles to Puget Sound. 

At the railroad crossing, Clover Creek varies from a low of 15 feet wide to 

about 40 feet wide at the ordinary high water mark (OHWM) (Photos 1 

and 2). The stream substrate is composed of gravels (1-3 inches in 

diameter, moderately imbedded) with a few cobbles (6-12 inches in 

diameter). Habitat in the creek within the study area is largely riffle type. 

Vegetative cover on the creek banks is approximately 50 percent. The tree 

canopy includes black cottonwood, red alder, and cherry (Prunus sp.), 

with an understory dominated by Himalayan blackberry, Indian plum 

(Oemleria cerasiformis), and bittersweet nightshade (Solanum 

dulcamara). In the study area, steelhead, coho salmon, Pacific lamprey, 

cutthroat trout, and rainbow trout are documented in Clover Creek. 

Photo 1. Clover Creek facing west (HDR 2007) Photo 2. Clover Creek facing north (2011)
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 15 

Stream 2 (Unnamed Tributary to American Lake) 

Stream 2 begins in a series of wetlands located on JBLM east of I-5. It is 

culverted under both I-5 and the railroad fill prism just south of North 

Thorne Lane Southwest where the stream daylights between fill prisms on 

all four sides, in which depression the stream inundates the lowermost 

portions, forming Wetland A (Photos 3 and 4). The stream exits Wetland 

A through a culvert toward the west under Union Avenue Southwest. West 

of Union Avenue Southwest, the stream travels approximately 1,000 feet 

before entering another long culvert that conveys flow into American 

Lake. 

Within Wetland A, Stream 2 is shallow and up to 150 feet wide. The 

channel is poorly defined, and substrate is largely sands with some areas 

of gravels (1-3 inches in size, 70 percent embedded) and spalls that have 

fallen from the railroad embankment. Habitat is largely run type, but 

backwater areas are present on either side of the stream. 

Photo 3. Stream 2 and Wetland A, facing 

west from railroad line (HDR 2007) 

Photo 4. Stream 2 and Wetland A, facing 

southeast from Union Avenue Southwest 

(2011) 

Fine organic debris is common in the water, and the channel is well 

shaded by vegetation. Species present include black cottonwood (Populus 

balsamifera) and Pacific willow (Salix lucida var. lasiandra) in the 

canopy and Himalayan blackberry (Rubus armeniacus) and red-osier 

dogwood (Cornus sericea) in the understory. No fish are documented in 

Stream 2. 

Murray Creek 

The contributing basin of Murray Creek largely occurs within vegetated 

open space east of I-5 within the boundary of JBLM. 
September 2012 Point Defiance Bypass Project 

Page 16 Fish, Wildlife, and Vegetation Discipline Report 

The creek flows toward the west and is culverted under both I-5 and the 

railroad (Photos 5 and 6). Between I-5 and the railroad, the creek flows 

through a channel dominated by emergent vegetation. 

Photo 5. Murray Creek facing west (HDR 2007) Photo 6. Murray Creek facing northeast (2011) 

The channel is approximately 25 feet wide and an estimated three feet 

deep. Habitat in this area is entirely pool type. Vegetative cover on the 

banks is dominated by common cattail (Typha latifolia) and reed 

canarygrass (Phalaris arundinacea). West of the railroad, Murray Creek 

flows about 3,000 feet before entering American Lake. Cutthroat trout are 

documented as occurring in the creek. 

Stream 3 (Unnamed Tributary to the Nisqually River) 

Stream 3 is located at the southern end of the Project, just south of the 

intersection of the rail line and Nisqually Road Southwest. Stream 3 

originates in a series of seeps on a steep slope east of the railroad right-ofway. The stream coalesces into a defined channel, approximately 5-15 feet 

in width at the OHWM, and about six inches deep (Photos 7 and 8). The 

channel runs about 200 feet along the toe of the railroad ballast slope 

where a debris dam creates a broad backwater area, approximately 20 feet 

wide, 50 feet long, and three feet deep (Wetland AB), before water exits 

through a five-foot diameter concrete culvert. The creek continues 

westward where it enters the Nisqually River floodplain, approximately 

100 feet below the railroad. 

The substrate of Stream 3 is largely silt, with some small areas of gravel 

(1-3 inches in size and highly embedded). Organic debris (twigs and 

leaves) are common in the stream. The habitat is mostly runs type, with a 

few smaller pools and a single large pool just upstream of the culvert. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 17 

Photo 7. Stream 3 and Wetland AB east of 

railroad, facing south (HDR 2007) 

Photo 8. Stream 3 and Wetland AB east of 

railroad, facing east from existing railroad 

(2011) 

Vegetative cover is approximately 100 percent. The canopy is dominated 

by red alder (Alnus rubra), although Douglas fir (Pseudotsuga menziesii) 

and western red cedar (Thuja plicata) are present upslope to the east. The 

understory is predominantly salmonberry (Rubus spectabilis) and vine 

maple (Acer circinatum). Sword fern (Polystichum munitum), licorice fern 

(Polypodium glycyrrhiza), bracken fern (Pteridium aquilinum), stinging 

nettle (Urtica dioica), youth-on-age (Tolmiea menziesii), and scouring 

rush (Equisetum hyemale) are common in the herbaceous layer. No fish 

are documented in Stream 3. 

Fish Presence in the Study Area 

This section outlines the potential for fish species tracked by NOAA 

Fisheries (Chinook, steelhead, coho, chum, and sockeye) to occur within 

the study area. A discussion on bull trout, regulated under the ESA by the 

USFWS, is also included. 

Exhibit 3 presents the fish species listed under the ESA in the Puget Sound 

region. 

Exhibit 3. Federally Listed Fish Species of the Puget Sound Region 

Species ESU * or DPS * Federal Status * 

Critical Habitat in the 

Study Area 

bull trout Coastal-Puget Sound FT No 

Chinook salmon Puget Sound FT No 

chum salmon Puget Sound/Strait of Georgia NW No 

coho salmon Puget Sound/Strait of Georgia FSC No 

steelhead Puget Sound FT No 

* (ESU) Evolutionarily Significant Unit; (DPS) Distinct Population Segment; (FT) Federal 

Threatened; (FSC) Federal Species of Concern; (NW) Not Warranted 
September 2012 Point Defiance Bypass Project 

Page 18 Fish, Wildlife, and Vegetation Discipline Report 

Exhibit 4 lists those fish species that may occur in streams that cross the 

study area. 

Exhibit 4. Fish Presence within the Study Area 

Stream Name 

Salmon and 

Steelhead Presence

(Listing Status*) 

Critical Habitat 

Present Other Resident Fishes 

Stream 1 none No none 

Clover Creek steelhead (FT) 

coho (FSC) No cutthroat trout, rainbow trout, 

Pacific lamprey (FSC, SM) 

Stream 2 none No none 

Murray Creek none No cutthroat trout 

Stream 3 none No none 

* (FT) Federal Threatened; (FSC) Federal Species of Concern, (SM) State Monitor 

No bull trout populations or residents are known to be present in any of 

the creeks that cross the study area (Nauer, 2000). Extensive studies in 

American Lake and Sequalitchew Lake have included gill netting and 

electroshocking, none of which have found bull trout (Sound Transit, 

2002). 

Stream 1, Stream 2, and Stream 3 

Stream 1 occurs entirely below grade at the Project crossing and does not 

provide fish habitat. No fish are documented in the stream and none were 

observed during field surveys. 

Stream 2, a tributary to American Lake, is inaccessible to anadramous fish 

(Sound Transit, 2002; D. Johnston, Personal Communications, 2006). No 

fish are documented in the stream and none were observed during field 

surveys. 

Stream 3 leaves the study area in an approximately 100-foot, smooth 

concrete culvert that does not appear to provide fish passage. No fish are 

documented in the stream and none were observed during field surveys. 

Murray Creek 

Murray Creek is not accessible to anadramous fish (Sound Transit, 2002; 

D. Johnston, Personal Communications, 2006). Although steelhead have 

been reported in American Lake downstream of the Project (D. Johnston, 

Personal Communications, 2006), none are known to utilize Murray Creek 

at the railroad crossing. The only species documented in the creek is 

cutthroat trout. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 19 

Clover Creek 

Clover Creek is the only waterway in the study area that is passable to 

anadramous fish. 

Although Clover Creek is passable to Chinook salmon, none are known 

to utilize the creek reach in the study area. Steelhead are documented in 

Clover Creek, and habitat is present in the study area (Nauer, 2000; Sound 

Transit, 2002). Spawning habitat for coho salmon is present in Clover 

Creek, and the stream reach within the study area appears to provide 

habitat suitable for foraging and rearing as well. Habitat for chum salmon

is present in Clover Creek in the study area (Nauer, 2000; Sound Transit, 

2002), but chum presence is not documented. Habitat for sockeye salmon

may be present in Clover Creek, but no sockeye are known to be present. 

Conclusion 

Steelhead (FT), coho salmon (FSC), and the Pacific lamprey (FSC) are the 

only listed species that may occur within the study area, all of which are 

documented in Clover Creek. 

Wildlife Habitat in the Study Area 

The study area is confined to a highly developed region surrounded by 

commercial and residential properties, military bases, and roadways. As a 

result, most of the habitat in the Project vicinity is fragmented. Vegetation 

in the study area generally occurs at or near the edge of the railroad rightof-way, which is managed (sprayed, mowed) for railroad operations. As a 

result, the study area provides poor habitat for most wildlife species, 

except those that have adapted to urban areas. Wildlife likely to be 

observed in the study area includes, but is not limited to, birds, rodents, 

raccoons, and feral cats and dogs. 

Wildlife Presence in the Study Area 

The following wildlife species and critical habitats are listed by the 

USFWS (2011) as occurring within Pierce County (see Exhibit 5). 
September 2012 Point Defiance Bypass Project 

Page 20 Fish, Wildlife, and Vegetation Discipline Report 

Exhibit 5. Listed Wildlife Species and Critical Habitats in Pierce County 

Species 

Regulatory 

Status 

Canada lynx (Lynx canadensis) FT, ST 

gray wolf (Canis lupus) FE, SE 

grizzly bear (Ursus arctos = U. a. horribilis) FT, SE 

marbled murrelet (Brachyramphus marmoratus) FT, ST 

northern spotted owl (Strix occidentalis caurina) FT, SE 

fisher (Martes pennant) FC, SE 

Mardon skipper (Polites mardon) FC, SE 

Roy Prairie and Tacoma Mazama pocket gopher, 

(Thomomys mazama ssp. glacialis and tacomensis) [historic] FC, ST 

North American wolverine (Gulo gulo luteus) Contiguous US DPS FC, SC 

Oregon spotted frog (Rana pretiosa) FC, SE 

streaked horned lark (Eremophila alpestris strigata) FC, SE 

Taylor’s checkerspot (Euphydryas editha taylori) FC, SE 

yellow-billed cuckoo (Coccyzus americanus) FC, SC 

bald eagle (Haliaeetus leucocephalus) FSC, SS 

Cascades frog (Rana cascadae) FSC 

Fender’s soliperlan stonefly (Soliperla fender) FSC 

Larch Mountain salamander (Plethodon larselli) FSC, SS 

long-eared myotis (Myotis evotis) FSC 

long-legged myotis (Myotis volans) FSC 

northern goshawk (Accipiter gentilis) FSC, SC 

northern sea otter (Enhydra lutris kenyoni) FSC, SE 

northwestern pond turtle (Clemmys marmorata ssp. marmorata) FSC 

olive-sided flycatcher (Contopus cooperi) FSC 

Oregon vesper sparrow (Pooectetes gramineus affinis) FSC, SC 

Pacific lamprey (Lampetra tridentata) FSC 

Pacific Townsend’s big-eared bat (Corynorhinus townsendii townsendii) FSC, SC 

peregrine falcon (Falco peregrines) FSC, SS 

river lamprey (Lampetra ayresi) FSC, SC 

slender-billed white-breasted nuthatch (Sitta carolinensis aculeate) FSC, SC 

tailed frog (Ascaphus truei) FSC 

valley silverspot butterfly (Speyeria zerene bremeri) FSC, SC 

western gray squirrel (Scirius griseus griseus) FSC, ST 

Van Dyke’s salamander (Plethodon vandykei) FSC, SC 

Critical Habitat (Species) Present in Study Area 

bull trout No 

marbled murrelet No 

northern spotted owl No 

(FE) Federal Endangered; (FT) Federal Threatened; (FC) Federal Candidate; (FSC) 

Federal Species of Concern; (SE) State Endangered; (ST) State Threatened; (SC) State 

Candidate; (SS) State Sensitive 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 21 

According to field survey data and background research, no Federallylisted species are documented within the study area. Bald eagles (FSC) 

nest outside the study area on the southeast shore of American Lake, over 

600 feet from the right-of-way. The nests are not visible from the railroad 

due to screening by trees and large buildings. Thus, the Project is not 

likely to disturb nesting eagles per thresholds outlined in the National 

Bald Eagle Management Guidelines (USFWS 2007). 

Vegetation in the Study Area 

The study area is located in the northern portion of the Puget Trough 

physiographic province of western Washington. The Puget Trough 

extends from the US/Canada border to the Willamette Valley between the 

Olympic Peninsula and the Cascade Mountain range. Puget Sound is the 

primary feature in the northern portion, and the Cowlitz River valley and 

part of the Chehalis River basin occupy the southern portion of the trough. 

The northern portion of the Puget Trough is a glaciated depression formed 

primarily by the extension of Cordilleran and continental glaciers during 

the Pleistocene Era. The trough is flat with moderate relief and is 

dominated by glacial deposits. 

Most of the study area is developed. The developed areas include 

commercial and residential properties, military bases (JBLM and Camp 

Murray), and roads. Thus, most of the study area has little to no 

vegetation, and provides little habitat for wildlife. Vegetation generally 

occurs at or near the edge of the railroad right-of-way. 

Vegetation types located in the study area include maintained vegetation, 

disturbed mixed forest, scattered trees, and wetland vegetation. Vegetation 

was identified and mapped based on aerial photo interpretation, 

supplemented with reconnaissance-level surveys within the railroad rightof-way. Each vegetation type is described below. 

Maintained Vegetation 

Maintained vegetation consists of vegetation managed (mowed, trimmed 

or treated with herbicide) along roadways and railroads for safety purposes 

(Photo 9). Maintained vegetation is the dominant vegetation type in the 

study area and is most dense past the toe of the railroad embankment. 

Dominant species include Scotch broom (Cytisus scoparius) (a noxious 

weed in Pierce County), Himalayan blackberry (Rubus armeniancus), and 

mixed grasses. 
September 2012 Point Defiance Bypass Project 

Page 22 Fish, Wildlife, and Vegetation Discipline Report 

Disturbed Mixed Forests 

Disturbed mixed forests are tree stands that have been altered by 

development, including thinning, trimming, and/or fragmentation. Such 

disturbed forests are scattered throughout the study area. In the northern 

portion of the study area, dominant trees are Douglas fir (Pseudotsuga 

menziesii), Pacific madrone (Arbutus menziesii), Lombardi poplar 

(Populus nigra) and Oregon white oak (Quercus garryiana). Scotch 

broom and Himalayan blackberry comprise the understory in some 

forested areas. 

Tree composition changes toward the southern end of the study area 

(Photo 10) where dominant trees include Douglas fir, red alder (Alnus 

rubra), and big-leaf maple (Acer macrophyllum), with an understory of 

salmonberry (Rubus spectabilis), red elderberry (Sambucus racemosa), 

snowberry (Symphoricarpos albus), and sword fern (Polystichum 

munitum). 

Photo 9. Maintained vegetation and scattered 

trees within the right-of-way near Clover 

Creek (2011) 

Photo 10. Disturbed mixed forest in the rightof-way near Nisqually Road (2007) 

Scattered Trees 

Scattered trees consist of small stands of trees comprised of a single 

species (Photo 9). Common species include Douglas fir, Pacific madrone, 

and Oregon white oak. 

Wetland Vegetation 

Four wetlands were identified in the study area (see Exhibit 6), 

collectively supporting a variety of trees, shrubs, and emergent plants. No 

effects are expected to occur in these wetlands or their buffers because 

they lie outside the Project footprint. Refer to the Wetlands Discipline 

Report for more details. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 23 

Exhibit 6. Wetlands in the Study Area 

Wetland 

ID 

Cowardin 

Classification1 and 

HGM Class2

Estimated Size 

(Acres)3 Rating Dominant Vegetation 

A Palustrine Scrub-shrub, 

Depressional 0.27 III 

Pacific willow, Himalayan 

blackberry, purple loosestrife, 

softstem bulrush, common cattail, 

and reed canarygrass 

E Palustrine Emergent, 

Riverine 0.3 III common cattail, reed canarygrass 

C Palustrine Forested, 

Slope 1.7 IV red alder, Himalayan blackberry, 

and scouring rush 

AB Palustrine Forested, 

Slope 1.2 III red alder, salmonberry, and youth-on-age 

1 Cowardin et al. (1979). 

2

 Hydrogeomorphic (HGM) Class (Brinson 1993). 

3 Wetland sizes are based on GIS estimates. 

ESA-Listed Plants 

Nine plant species are listed by the USFWS and WDNR for Pierce County 

(see Exhibit 7). Based on vegetation communities and habitats observed 

during site visits, it is unlikely that any listed plant occurs in the study 

area. 

Exhibit 7. Federal and State-Listed Plants in Pierce County 

Common Name Scientific Name 

Regulatory 

Status 

clustered lady’s slipper Cypripedium fasiculatum FSC/SS 

golden paintbrush Castilleja levisecta FT/SE 

marsh sandwort Arenaria paludicola FE/X 

obscure paintbrush Castilleja cryptantha FSC/SS 

tall bugbane Cimicifuga elata FSC/SS 

Torrey’s peavine Lathyrus torreyi FSC/ST 

triangular-lobed moonwort Botrychium ascendens FSC/SS 

water howellia Howellia aquatilis FT/ST 

white-top aster Aster curtus FSC/SS 

(FE) Federal Endangered; (FT) Federal Threatened; (FSC) Federal Species of Concern; 

(SE) State Endangered; (ST) State Threatened; (SS) State Sensitive; (X) possibly extinct or 

extirpated from Washington
September 2012 Point Defiance Bypass Project 

Page 24 Fish, Wildlife, and Vegetation Discipline Report 

Chapter 4 – Potential Project Effects 

This section summarizes the effects incurred by construction of the Build 

Alternative (the Project) or the No Build Alternative, based on review of 

the Project design in the context of existing baseline disturbance, available 

background information, and field data. 

Would fish, wildlife, or vegetation resources be impacted or 

affected? 

No Build Alternative 

No direct, indirect, or cumulative effects to fish, wildlife, or vegetation 

would result. Amtrak service would continue to operate on the Puget 

Sound route within a landscape disturbed by development and urban 

activity. No additional construction or maintenance activities would result 

from the No Build Alternative. 

Build Alternative 

Direct Effects 

Direct effects resulting from the Build Alternative include permanent 

vegetation clearing within the railroad right-of-way and elevated 

construction noise and visual disturbance. 

Approximately 24 acres of maintained vegetation, 2.5 acres of disturbed 

mixed forest, and one acre of scattered trees would be cleared within the 

railroad right-of-way. However, existing vegetation is fragmented, 

disturbed by rail operations and vegetation management, and does not 

provide habitat suitable for ESA-listed species. 

During construction, visual disturbance and elevated noise are expected to 

be marginally higher than baseline levels along the project corridor. As 

such, the Project could disturb terrestrial wildlife that may be present 

within the right-of-way, but, in the context of urban development, 

vehicular traffic on I-5 and local roads, and pedestrian activity, the effects 

of the Build Alternative on fish, wildlife, and vegetation, including ESAlisted species, is expected to be discountable. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 25 

Indirect Effects 

The Project is located within an existing rail corridor and urbanized area. 

The only potential indirect effect tied to the Project is that it may 

indirectly influence redevelopment near the relocated Amtrak Station at 

Freighthouse Square (see Land Use Discipline Report12). Such 

redevelopment would be consistent with local zoning and approved by 

state and local agencies and would take place in previously disturbed areas 

where fish, wildlife, and vegetation are not present. Thus, no indirect 

effects to these resources are expected. 

Cumulative Effects 

The Project would have no direct or indirect effect on fish or wildlife. The 

Project would have a minor, short-term construction effect on the 

vegetation along the rail right of way which will not lead to long-term 

impacts. FRA and WSDOT considered the Project’s minimization 

measures for effects to vegetation in combination with other current and 

future projects that provide habitat improvements such as the Nisqually 

National Wildlife Refuge, environmental projects on JBLM, and local 

agencies’ critical area ordinances. FRA and WSDOT found that the 

Project’s vegetation measures are adequate to ensure no contribution to an 

adverse cumulative effect. 

 12 WSDOT 2012
September 2012 Point Defiance Bypass Project 

Page 26 Fish, Wildlife, and Vegetation Discipline Report 

Chapter 5 – Recommended 

Minimization Measures 

As noted previously, no significant effects to fish, wildlife, or vegetative 

resources are anticipated. This chapter provides Best Management 

Practices (BMPs) that could be applied during construction to minimize 

the Project’s effects. 

What minimization is required for the No Build Alternative? 

No minimization is proposed under the No Build Alternative since there 

would be no effects to fish, wildlife, or vegetative resources. 

What minimization is required for the Build Alternative? 

The following BMPs for the Build Alternative focus on minimization of 

potential construction effects: 

 Construction effects will be confined to the minimum area 

necessary to complete the Project and clearing limits will be 

clearly marked by staking done by the contractor’s surveyor. Areas 

of landscape or vegetative preservation will be protected with 

construction fencing. 

 Removal of native vegetation will be minimized to the greatest 

extent possible. 

 A Temporary Sediment and Erosion Control (TESC) Plan and 

Stormwater Site Plan will be developed and implemented for all 

projects requiring clearing, vegetation removal, grading, ditching, 

filling, embankment compaction or excavation. The BMPs in the 

plans will be used to control sediments from all vegetation or 

ground disturbing activities. 

 BMPs will be implemented for construction activities that occur 

within 200 feet of surface water or wetland habitat as identified by 

the Project biologist, to ensure that no foreign material, such as 

railroad ballast or other material is sidecast, and to control and 

prevent sediments from entering aquatic systems. 

 No contractor staging areas will be allowed within 300 feet of any 

jurisdictional wetland, stream, river, or drainage, as identified by 

the Project biologist, unless site-specific review completed by the 

Project biologist indicates that no effects to the sensitive resource 

areas will occur due to topography or other factors. 
Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 27 

 Application of chemicals such as fertilizers and pesticides will be 

conducted in a manner and at application rates that will not result 

in loss of chemicals to stormwater runoff. 

 Highly turbid or contaminated dewatering water will be handled 

separately from stormwater and not allowed to enter local drainage 

systems. 

Point Defiance Bypass Project September 2012 

Fish, Wildlife, and Vegetation Discipline Report Page 29 

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