Appendix I: 

Water Resources

Discipline Report

Point Defiance Bypass 

Project

Water Resources

Discipline Report

September 2012

Point Defiance Bypass Project September 2012

Water Resources Discipline Report Page i

Table of Contents

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

What are the water resources in the study area? 1

How would the Project affect water resources? 2

Would the Project need minimization measures related to water resources? 3

Chapter 1 – Project Description .......................................................................................................................5

Introduction 5

Purpose and Need 5

What alternatives are being considered for the Point Defiance Bypass Project? 6

What’s happening in the bypass corridor today? 6

What would happen if the Project were not built? 7

What are the proposed improvements and related activities of the Point Defiance Bypass 

Project? 7

What are the proposed operational changes that would result from the Point Defiance 

Bypass Project? 8

Chapter 2 – Methodology...............................................................................................................................11

What is included in the water resources analysis? 11

How was the study area defined? 11

What design guidance was used in reference to the Project? 11

How were the Project’s effects on water resources evaluated? 13

Chapter 3 – Studies and Coordination ...........................................................................................................15

How does this report relate to previous environmental studies completed for the Project? 15

What coordination took place as part of the water resources analysis? 15

What regulations apply to water resources in the study area? 16

Chapter 4 – Affected Environment .................................................................................................................19

What surface waters are present in the study area? 19

Are there regulated shorelines in the study area? 24

Where are the areas at risk for flooding in the study area? 24

What is the condition of groundwater in the study area? 26

Chapter 5 – Project Effects ............................................................................................................................29

What is considered a “project effect?” 29

How would the No Build Alternative affect water resources? 29

How would the Project directly affect water resources during construction? 29

How would the Project directly affect water resources after it is built? 31

What potential indirect effects could occur from the Project? 34

What cumulative effects would there be from the Project and other planned projects in 

the study area? 34

Does the Project cause any significant unavoidable adverse effects? 34

Chapter 6 – Recommended Minimization Measures......................................................................................35

What is considered “minimization?” 35

What measures will be taken to minimize the effects during construction of the Project? 35

How will operational effects be minimized? 37
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References.....................................................................................................................................................39

List of Exhibits

Exhibit 1. Build Alternative Components ........................................................................................... 9

Exhibit 2. Surface Water Resources ............................................................................................... 20

Exhibit 3. Floodplains ...................................................................................................................... 25

Exhibit 4. Groundwater Resources.................................................................................................. 27
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Summary

What are the water resources in the study area?

Surface Water

The Point Defiance Bypass Project (the Project) would occur within three 

major watersheds known as the Puyallup/White, Chambers/ Clover, and 

Nisqually Water Resource Inventory Areas (WRIAs). Within the study 

area WRIAs, the Project would cross seven watercourses of interest:

• First Creek: An urbanized stream network managed by the City of 

Tacoma as a stormwater conveyance system and utility corridor. 

First Creek flows through the study area in a 6-foot-diameter pipe 

before discharging to the Puyallup River.

• Tacoma Eastern Gulch/B-Street Gulch: A large open channel 

that is typically dry, but may convey flows to the Thea Foss 

Waterway during large storms. The gulch flows are conveyed 

through the study area in a 6-foot-diameter culvert.

• Stream 1: A small tributary stream to Flett Creek that crosses the 

project corridor through a 3-foot-diameter culvert.

• Clover Creek: The largest stream in the study area, with 

documented water quality problems related to fecal coliform 

bacteria.

1 The existing rail line crosses over the stream on a 70-

foot-long wood trestle bridge.

• Stream 2: A small tributary stream to American Lake that only 

flows during certain times of the year. Though it is a small, 

intermittent stream, it has an associated 500-year floodplain and 

crosses the study area in a 5-foot-diameter culvert.

• Murray Creek: A continuously-flowing tributary stream to 

American Lake that crosses the study area in a 9-foot-diameter 

culvert.

• Stream 3: A small tributary to the Nisqually River that only flows 

during certain times of the year. It passes through the study area in

a 3-foot-diameter culvert.

 1 Ecology 2009a.
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Shorelines

Within the study area, the Puyallup River, Nisqually River, and American 

Lake have shorelines of statewide significance.2 Clover Creek, 

Sequalitchew Creek (which flows between American Lake and 

Sequalitchew Lake), and Gravelly Lake also have regulated shorelines.3

Floodplains

There are regulated 100- and 500-year floodplains associated with surface 

waters in the study area. The floodplains for Clover Creek and Murray 

Creek are regulated by the Federal Emergency Management Agency

(FEMA), while the floodplains for Streams 1 and 2 are flood hazard areas 

designated by Pierce County.

Groundwater

Because of the generally porous soils in the study area, groundwater may 

be susceptible to contamination from uncontrolled spills and other sources 

of pollution. The Project lies within a USEPA-designated sole source 

aquifer area. In addition, Pierce County has designated critical aquifer 

recharge and wellhead protection areas that occur within the study area. 

How would the Project affect water resources?

The effect on water resources from the No Build Alternative would be the 

same as existing conditions.

The Project would pose some risk to surface and groundwater from 

sediment transport and/or pollutant spills during construction. However, 

the Project would minimize or eliminate these risks through the 

implementation of required BMPs. Therefore, no construction effects are 

expected.

No direct effects to water resources are expected from operation of the 

Project. The Project would remove vegetation as part of track construction 

and reconstruction, and add new impervious surfaces for roadway and 

sidewalk upgrades. However, the changes in land cover would be below 

the thresholds for flow control and water quality treatment requirements 

outlined in WSDOT’s Highway Runoff Manual.

4 Therefore, in accordance 

with the presumptive approach, the Project is not expected to result in 

effects to surface waters through changes in volume or water quality. In 

 2 WAC 173-18-310, WAC 173-20-570. 3 WAC 173-18-310, WAC 173-20-560. 4 WSDOT 2010b.
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addition, no changes would be made within the boundaries of regulated 

shorelines or floodplains.

Would the Project need minimization measures related to 

water resources?

Minimization for potential construction-related water quality impacts 

would be addressed by complying with the National Pollution Discharge 

Elimination System Construction Stormwater General Permit process,

5

and Highway Runoff Manual standards and best management practices,

6

as appropriate.

 5 Ecology 2010a.

6 WSDOT 2010b.
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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.7 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...”8.

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. 

 7 The three owners of the project corridor are Sound Transit, Tacoma Rail, and BNSF. 8 WSDOT 2009
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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 
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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-
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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.
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Exhibit 1. Build Alternative Components
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Chapter 2 – Methodology

What is included in the water resources analysis?

This report discusses the existing water resources in the vicinity of the 

Project, how they would be affected by the Project, and what measures 

could be taken to minimize potential effects.

Water resources included in this analysis are:

• Surface waters, which include streams, rivers, and lakes

• Shorelines

• Floodplains

• Groundwater, which includes critical aquifer recharger areas, sole 

source aquifers, and wellhead protection areas

How was the study area defined?

The study area for the water resources analysis includes water resources 

that exist within the boundary of the Project footprint, their associated 

drainage basins, and downstream receiving waters. The study area was 

determined by reviewing existing aerial photography and geographic 

information system (GIS) data from federal, state, county, and local 

sources.

What design guidance was used in reference to the 

Project?

WSDOT has set forth minimum requirements in the Highway Runoff 

Manual (HRM), which have been approved by the Washington State 

Department of Ecology (Ecology), to achieve compliance with federal and 

state water quality regulations through the presumptive approach.9

Under the presumptive approach, projects meeting the thresholds in the 

HRM are expected to comply with local, state, and federal water qualitybased standards if they use the Best Management Practices (BMPs)

outlined in the HRM. Those projects falling below the thresholds are 

expected to meet applicable regulations without the use of additional 

 9 WSDOT 2010b.
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BMPs. In turn, projects that comply with local, state, and federal water 

quality-based standards are not expected to affect water resources.

The HRM requires general stormwater planning and management for most 

large projects. In addition, the HRM requires specific evaluation of a 

project for water quality treatment and flow control based on land use 

changes within each threshold discharge area (TDA). A TDA is an on-site 

area that drains to a single natural discharge location or multiple natural 

discharge locations that combine within a quarter mile downstream of the 

study area.

The HRM requires basic water quality treatment BMPs in any given 

project TDA that meets either of the following thresholds:

• The effective PGIS is greater than 5,000 square feet in a TDA. 

• For western Washington, the project converts three-quarters of an 

acre or more of native vegetation to pollution-generating pervious 

surface within a TDA and there is a surface discharge in a natural 

or manmade conveyance system from the site.

The HRM also requires flow control BMPs for the effective impervious 

surfaces and, in western Washington, the converted pervious surfaces in 

any project TDA that meets one or more of the following thresholds:

• The effective impervious surface is greater than 10,000 square feet 

in the TDA.

• In western Washington, the TDA converts three-quarters of an acre 

or more of native vegetation to lawn or landscaped area and there 

is a surface discharge in a natural or manmade conveyance system 

from the site.

• In western Washington, the combination of effective impervious 

surfaces and converted pervious surfaces in the TDA causes the 

100-year frequency flow to increase by 0.1 cubic foot per second 

or more.

FRA and WSDOT projects sometimes fall within the jurisdiction of other 

local governments that have more stringent standards than those outlined 

in the HRM. The project would be designed to meet the local requirements 

only if Ecology has required the local government to use more stringent 

standards, rather than the local jurisdiction simply doing so of its own 

accord. Within the study area, there are no known Ecology-required local 

requirements more stringent that those outlined in the HRM. Therefore, for 

the purposes of this study, it is assumed that the Project would mainly 

follow the surface water design guidelines in the HRM.
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How were the Project’s effects on water resources 

evaluated?

The existing conditions in the study area were used as a baseline to 

compare the potential changes from the Project. Existing conditions were 

identified using field observations, literature review, and aerial 

photographic analysis. The Project’s potential effects on water resources 

compared to the baseline were qualitatively evaluated based on regulatory 

guidance (see list in Chapter 3) and similar past projects.
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Chapter 3 – Studies and Coordination

How does this report relate to previous environmental 

studies completed for the Project?

This report builds upon environmental work previously conducted by FRA 

and WSDOT for the Project including:

• Point Defiance Bypass Project Hydrology and Water Quality 

Technical Memorandum10

• Point Defiance Rail Bypass Project Draft Floodplain Discipline 

Report11

• Point Defiance Bypass Project Fish, Wildlife, and Vegetation

Discipline Report12

• Point Defiance Bypass Project Soils and Geology Discipline 

Report13

Information for the water resources analysis was taken partially from the 

previous FRA and WSDOT studies and was supplemented through

literature review and with data from regulatory agency websites.

What coordination took place as part of the water 

resources analysis?

FRA and WSDOT coordinated with other authors on the Point Defiance 

Bypass team, including those responsible for the fish, wildlife, and 

vegetation; wetlands; and geology and soils analyses.

 10 WSDOT 2007. 11 WSDOT 2011a. 12 WSDOT 2011b. 13 WSDOT 2011c.
September 2012 Point Defiance Bypass Project

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Information was also collected from the following sources:

• Federal Emergency Management Agency (FEMA)

14

• US Environmental Protection Agency (USEPA)

15

• Ecology16

• Pierce County17

• City of Tacoma18

What regulations apply to water resources in the study 

area?

Regulations related to water resources that apply to the Project are listed 

below.

Federal

• National Environmental Policy Act, 42 USC Section 4321

• Clean Water Act, 33 USC 1251 et seq.

• Coastal Zone Management Act, 16 USC 1451 et seq.

• Floodplain Management Presidential Executive Order 11988

• Safe Drinking Water Act, 42 USC 300 et seq, Chapter 6A

State

• State Environmental Policy Act, WAC 197-11 and WAC 468-12 

• Water Pollution Control Act, RCW 90.48

• Water Quality Standards for Surface Waters, WAC 173-201A

• Water Quality Standards for Ground, WAC 173-200

• Shoreline Management Act, RCW 90.58, WAC 173-26

• Flood Control Management Act, RCW 89

• National Pollutant Discharge Elimination System (NPDES) 

Construction Stormwater General Permit 19

• WSDOT’s NPDES Municipal Stormwater Permit20

 14 FEMA 2011. 15 EPA 2011a,b,c. 16 Ecology 2009a. 17 Pierce County 2011a, 2011b. 18 Tacoma 2011a, 2011b. 19 Ecology 2010a. 20 Ecology 2009b.
Point Defiance Bypass Project September 2012

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Additional regulations related to water resources that apply to local 

jurisdictions within the study area are listed below.

• Pierce County Storm Drainage and Surface Water Management 

Code, PCC Title 11

• Pierce County Shoreline Management Use Regulations, PCC 

Title 20

• Pierce County Construction and Infrastructure Regulations for Site 

Development and Stormwater Drainage, PCC Title 17A

• Pierce County Development Regulations for Storm Drainage and 

Site Development, PCC Title 18C

• Pierce County Development Regulations for Critical Areas, PCC 

Title 18E

• NPDES Phase 1 Municipal Stormwater Permit, applicable to 

Pierce County and City of Tacoma21

• South Tacoma Groundwater Protection District, TMC

Chapter 13.09

As discussed in Chapter 2, the Project would comply with state and 

federal requirements by following the guidance contained in the HRM. 

The local requirements listed above not expected to meet any additional 

federal or state requirements beyond those met through use of the HRM.

 21 Ecology 2010b.
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Chapter 4 – Affected Environment

What surface waters are present in the study area?

The surface water analysis was grouped according to the three Water 

Resource Inventory Areas (WRIAs) in which the study area occurs. The 

WRIAs are, from north to south:

• WRIA 10 Puyallup/White

• WRIA 12 Chambers/Clover

• WRIA 11 Nisqually 

These WRIAs represent the major watersheds for surface water in the 

study area. Within these WRIAs, the Project would cross seven 

watercourses of interest, which are described in the following sections. 

The study area basins, associated WRIAs, and watercourses of interest are 

shown on Exhibit 2.

WRIA 10 Puyallup/White

The Puyallup River Watershed is the largest watershed in Pierce County, 

covering over 622,000 acres and including all lands tributary to the 

Puyallup, Carbon, and White Rivers.

22 The lower part of the watershed 

where the study area is located is affected by urban stressors, such as road 

and stormwater runoff, other sources of pollution, conversion of open 

space to development, and permanent removal of vegetation.23 In the 

lower Puyallup tideflats area, industrial activity is dominant.

The river, along with its tributaries, serve as major migration routes for a 

variety of salmonids, including spring Chinook salmon (Oncorhynchus 

tshawytscha) and bull trout (Salvelinus confluentus), which have both been 

listed as endangered species under the Endangered Species Act (ESA). 

There are four fish hatcheries located in the Puyallup River Watershed 

upstream of the study area.24

 22 Ecology 1995a. 23 Pierce County 2011a. 24 Tacoma 2008.
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Exhibit 2. Surface Water Resources
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Within the study area, the Puyallup River is not identified on Ecology’s 

303(d) list for exceedance of any water quality standards.25

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 East 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-5.26

Tacoma Eastern Gulch / “A” Street Gully

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 alignment through a 6-footdiameter culvert before discharging into the Thea Foss Waterway.

27 No 

natural or critical area habitat is associated with the Tacoma Eastern 

Gulch.

The Foss Waterway sub-basin covers approximately 5,780 acres in southcentral Tacoma. This sub-basin is mostly residential, with some 

commercial and industrial land use.

28

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.29

WRIA 12 Chambers/Clover

The Chambers/Clover Creek Watershed covers approximately 92,160 

acres and receives runoff from the most urbanized portion of Pierce 

County.

30 It receives drainage flows from seven municipalities (Tacoma, 

Ruston, Fircrest, University Place, Lakewood, Steilacoom, and DuPont), 

Camp Murray, and the northern segment of JBLM. Urbanization in this 

watershed has resulted in stream degradation from effects such as heavy 

recreational use, increase in impervious surfaces, clearing of streamside 

 25 Ecology 2009a. 26 Tacoma 2011c. 27 Federal Transit Administration 2002. 28 Tacoma 2011b. 29 Ecology 2009a. 30 Ecology 1995b.
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vegetation, pet waste, vehicle emissions and leaks, pesticide and fertilizer 

use, leaking from underground storage tanks, and untreated urban and 

stormwater runoff.31

Stream 1, Flett Creek Tributary

Stream 1, an unnamed tributary to Flett Creek, crosses the project corridor 

through a 3-foot-diameter corrugated steel culvert located between SE 74th

Street and SE 80th Street in the City of Tacoma, near Rail MP 7.65.

32 This 

stream drains the urban area to the east of South Tacoma Way and east to 

the east side of I-5. The Flett Creek sub-basin comprises 7,153 acres, with 

runoff coming from mostly residential areas and some commercial and 

industrial areas.33 Flett Creek flows into Chambers Creek, a salmonidbearing stream, that discharges into Chambers Bay and then into the 

Narrows.34

Within the study area, Stream 1 is not identified on Ecology’s 303(d) list 

for exceedance of any water quality standards.35

Infiltration of stormwater runoff from PGIS is generally prohibited in this 

area by the South Tacoma Groundwater Protection District. 

Clover Creek

Clover Creek is the largest perennial stream in the study area with a 

drainage area of approximately 47,400 acres. The Clover Creek channel

crosses under the existing rail line just south of Bridgeport Way Southwest

at Rail MP 10.8 beneath a 70-foot-long wood trestle bridge. Clover Creek

is a fish-bearing stream originating from springs and groundwater 

discharge in the northeast corner of the watershed and that flows into 

Steilacoom Lake. Steilacoom Lake is the source of Chambers Creek, while 

Leach Creek and Flett Creek are two important tributaries to Chambers 

Creek. Chambers Creek flows north and west down a ravine into 

Chambers Bay, then into Puget Sound. Clover Creek is the only gauged 

stream in the study area.36

Within the study area, Clover Creek is identified on Ecology’s 303(d) list 

as exceeding water quality standards for fecal coliform bacteria.

37

 31 Pierce County 2011a. 32 WSDOT 2011a. 33 Tacoma 2011b. 34 Tacoma 2011b. 35 Ecology 2009a. 36 WSDOT 2007, WSDOT 2011a. 37 Ecology 2009a.
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Stream 2, American Lake Tributary

Stream 2, a small intermittent tributary to American Lake, crosses the

Project right-of-way just south of N. Thorne Lane Southwest at Rail MP 

12.85 in a 5-foot-diameter circular concrete culvert.38

American Lake, the largest natural lake in Pierce County, is approximately 

1,100 acres in size with a drainage area of approximately 4,200 acres.

39 It 

is supplied by groundwater and Murray Creek, and has a controlled 

outflow to Sequalitchew Creek. The lake receives heavy recreational 

use.40

American Lake is identified on Ecology’s 303(d) list as exceeding water 

quality standards for total phosphorus and various toxins in tissue 

samples.41

Murray Creek

Murray Creek is a perennial tributary to American Lake that has a 

drainage area of approximately 10,240 acres.

42 The stream channel crosses 

the BNSF right-of-way just south of Berkeley Street Southwest at Rail MP 

14.0 in a 9-foot-diameter circular concrete culvert.43

Within the study area, Murray Creek is not identified on Ecology’s 303(d) 

list for exceedance of any water quality standards.44

WRIA 11 Nisqually

Stream 3, Nisqually River Tributary

Stream 3, the only surface water in the study area located in the 486,400-

acre Nisqually Watershed (WRIA 11), is an intermittent, spring-fed 

stream. 45 Stream 3 crosses the Project right-of-way just south of the 

intersection of the rail line and Nisqually Road Southwest at Rail MP 

21.25 in a 3-foot-diameter circular corrugated steel culvert.46

Within the study area, neither the Nisqually River nor Stream 3 is

identified on Ecology’s 303(d) list for exceedance of any water quality 

standards.47

 38 WSDOT 2011a. 39 Ecology 1995b. 40 Pierce County 2011. 41 Ecology 2009a. 42 Pierce County 2011b. 43 WSDOT 2011a. 44 Ecology 2009a. 45 Pierce County 2006. 46 WSDOT 2011a. 47 Ecology 2009a.
September 2012 Point Defiance Bypass Project

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Are there regulated shorelines in the study area?

Pierce County is the regulating authority for designated shorelines in the 

study area, including shorelines of statewide significance. Ecology 

designates shorelines of statewide significance to include areas within 200 

feet of river or stream segments in Western Washington where the mean 

annual flow is 1,000 cubic feet per second or more, and lakes that are

1,000 acres or more in size.

48 Pierce County also regulates shorelines of 

river or stream segments where the mean annual flow is greater than 20 

cubic feet per second and shorelines on lakes greater than or equal to 20 

acres in size.49 Along regulated shorelines, Pierce County limits and/or 

prohibits certain developments and activities.

Within the study area, the Puyallup River, Nisqually River, and American 

Lake have shorelines of statewide significance.

50 Clover Creek, 

Sequalitchew Creek, and Gravelly Lake also have regulated shorelines.51

Where are the areas at risk for flooding in the study area?

Designated 100-year and 500-year floodplains in the study area are shown 

in Exhibit 3. Within the study area, Clover Creek and Murray Creek have 

flood zones regulated by FEMA. These flood zones are geographic areas 

defined by FEMA as having an annual risk of flooding of 1 percent (100-

year floodplain) or 0.2 percent (500-year floodplain).52

First Creek, Stream 1, and Stream 2 do not have FEMA flood zones, but 

they do have flood hazard areas designated by Pierce County. Pierce 

County designates flood hazard areas as those identified by FEMA, but 

also areas within 65 feet from the ordinary high water mark of an 

identified natural river, stream, or other water channel; areas within 10

vertical feet from the bottom of a regulated closed depression; areas within 

two vertical feet of a potential surface water spillway or other type of 

outlet; and identified channel migration zones.53

The Tacoma Eastern Gulch and Stream 3 do not have either a designated 

FEMA flood zone or a Pierce County flood hazard area in the study area.

 48 RCW 90.58.030. 49 Pierce County Code§20.04.560. 50 WAC 173-18-310, WAC 173-20-570. 51 WAC 173-18-310, WAC 173-20-560. 52 FEMA 2011. 53 Pierce County Code§18E.70.020.
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Exhibit 3. Floodplains
September 2012 Point Defiance Bypass Project

Page 26 Water Resources Discipline Report

What is the condition of groundwater in the study area?

Groundwater Movement

The topography across most of the study area is generally flat and has 

underlying coarse-grained, permeable soils; therefore, most of the 

precipitation falling on the surface infiltrates directly into the ground. 

Water that infiltrates in the study area moves laterally through the shallow 

groundwater system, where the groundwater table is approximately 10-40 

feet below the ground surface. The water table commonly intersects larger 

depressions in the land surface, resulting in standing bodies like American 

Lake. Because of rapid infiltration and the shallow groundwater system, 

the groundwater in the study area is susceptible to contamination. This is 

especially true in the northern portion of the project corridor, from TR 

Junction (Rail MP 1.0) to Freighthouse Square, where groundwater is very 

shallow and highly susceptible to contamination.54

Sole Source Aquifers

As shown on Exhibit 4, the Project would lie within a USEPA-designated 

sole source aquifer area. A sole source aquifer is an aquifer that is either 

the main (it supplies over 50 percent of the total demand) or only source of 

drinking water consumed in the area above the aquifer. These areas have 

no alternative source(s) that can physically, legally, or economically 

supply drinking water to recipients who depend upon the aquifer.55 The 

USEPA reviews all federally-funded projects that may have the potential 

to contaminate a designated sole source aquifer.56

The USEPA designated the sole source aquifer shown in Exhibit 4 as the

Central Pierce County Aquifer System in 1989. The groundwater in this 

area moves regionally through unconsolidated glacial deposits toward 

Puget Sound and adjacent river valleys. Groundwater from the aquifer 

system supplies between 60 and 90 percent of the drinking water used 

within the area. The quality of drinking water supplied by the aquifer is 

generally good, but contamination is becoming more frequent and 

gradually decreasing the water quality.57

Critical Aquifer Recharge and Wellhead Protection Areas

The study area contains critical aquifer recharge and wellhead protection 

areas, which are shown in Exhibit 4.

 54 WSDOT 2011c. 55 EPA 2011a. 56 EPA 2011b. 57 EPA 2011c.
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Exhibit 4. Groundwater Resources
September 2012 Point Defiance Bypass Project

Page 28 Water Resources Discipline Report

Pierce County defines aquifer recharge areas as areas that have a critical 

effect on recharging groundwaters used for potable water supplies. These 

groundwater areas may also be at risk of contamination from land use 

activities. Wellhead protection area boundaries are defined by Pierce 

County as the maximum distance from which a contaminant could 

potentially reach a public water system well within 10 years of travel 

through the ground.

58

Within critical aquifer recharge and wellhead protection areas, Pierce 

County regulates the amount of impervious surface that may be added by 

new development. In addition, Pierce County prohibits and/or regulates

certain activities and land uses, such as landfills, underground injection 

wells, metals mining, wood treatment facilities, pesticide manufacturing, 

petroleum refining and/or storage facilities, hazardous product storage, 

and certain agricultural activities.59

Potential Pollutant Sources

The sandy and gravelly soils found in the eastern half of the 

Chambers/Clover Creek area are porous; therefore, pollutants may leach 

into the unconfined aquifer and enter the groundwater. Potential sources of 

pollutants in the watershed include uncontrolled roadway runoff, existing 

septic tanks, drain fields, solid waste disposal landfills, and underground 

storage tanks.

60

 58 Pierce County Code §18.25.030. 59 Pierce County Code §18E.50.040. 60 Pierce County 2011.
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Chapter 5 – Potential Project Effects

What is considered a “project effect?”

Effects from a project can be direct, indirect, or cumulative. Direct effects 

are effects caused by a project that occur at the same time and place, 

including construction of the project, changes in the landscape, and longterm operation of new facilities. Indirect effects caused by a project 

happen later in time or farther away. Cumulative effects result from the 

effects of one project that are then added to other past, present, and likely

future projects, regardless of who implements each project. Cumulative 

effects can result from individual small actions that become significant 

when added together in one place or over time.61

How would the No Build Alternative affect water 

resources?

No direct, indirect, or cumulative effects to water resources 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. 

How would the Project directly affect water resources 

during construction?

Construction Effects

Construction elements of the Project that were evaluated in the water 

resources study included the following:

• Between South 66th Street (Rail MP 6.9) to about 700 feet beyond 

the Lakewood Station (Rail MP 10.1), track ballast material would 

be added and new rail would be installed. Stream 1 crosses the 

Project alignment in this construction area.

• Between about 700 feet beyond the Lakewood Station (Rail 

MP 10.1) to the southern end of the Project, the track section 

 61 WSDOT 2010a.
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would be reconstructed. The reconstruction would involve clearing 

and grubbing the existing ground of vegetation, cutting into 

existing slopes, placing new fill for wider track embankments, 

excavating new drainage ditches, placing track sub-ballast and 

ballast material, and hauling away and disposing of excavated 

material. Clover Creek, Stream 2, Murray Creek, and Stream 3 

cross the project alignment in this reconstruction area. 

• Roadway upgrades would be implemented at Clover Creek Drive 

Southwest, North Thorne Lane Southwest, Berkeley Street 

Southwest, 41st Division Drive, and Barksdale Avenue. New 

impervious surfaces would be constructed at these crossings. The 

Clover Creek Drive Southwest construction would take place 

approximately 600 feet southwest of Clover Creek; the North 

Thorne Lane Southwest construction would take place 

approximately 200 feet northeast of Stream 2; and the Berkeley 

Street Southwest construction would take place approximately 

1,500 feet northeast of Murray Creek. The construction at 

41st Division Drive and Barksdale Avenue would not be 

immediately adjacent to any streams in the study area.

• At the two bridges crossing I-5 near Rail MP 20.0, additional 

construction along the rail line could potentially include extending 

the bridge abutment wing walls with retaining structures, which 

could require high cuts into existing slopes. Additional 

construction activities could include protecting the track from 

upslope debris and removal of existing loose fill. No streams are in 

the immediate vicinity of this construction area.

• In the vicinity of the Mounts Road overpass (Rail MP 19.8), the 

track embankment slopes could potentially be regraded and new 

retaining structures may be installed to support the track widening. 

No streams are in the immediate vicinity of this construction area.

• At Freighthouse Square, modifications to the station would involve 

reconstructing a portion of the existing Freighthouse Square 

building, extending or rebuilding the existing commuter rail 

platform, modifying existing on-street parking and parking lots, 

and creating additional parking. Freighthouse Square is 

approximately 900 feet east of the Tacoma Eastern Gulch.

Effect Evaluation

Effects to water resources from construction-related activities were 

evaluated in the context that the Project would comply with applicable 

requirements of the NPDES Construction Stormwater General Permit

process,

62 and HRM standards and BMPs,63 as appropriate.

 62 Ecology 2010a. 63 WSDOT 2010b.
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Construction effects on surface water can result from the types of 

earthwork, concrete work, paving, stockpiling, material transport, and 

storm drainage utility work planned as part of the Project. Soil exposed in 

sloped excavations or fills would be especially susceptible to local erosion 

until vegetation was established. In addition, if the exposed soil dries out, 

it can also be at risk from wind erosion. Eroded soil can be carried by 

water or wind into adjacent stormwater drains and streams. Also, the pH in 

surface water can be increased if runoff comes in contact with curing 

concrete. The tires of construction vehicles could also carry soil onto 

roadways, which could then runoff into ditches or streams. In addition, 

equipment leaks or spills from construction machinery can also affect

water quality in nearby water resources. Construction-related pollutants 

can increase turbidity and affect other water quality parameters, such as 

pH levels and/or the amount of available oxygen in the water. However, as 

discussed in Chapter 6, construction pollution-prevention BMPs would be 

implemented to avoid and minimize the risk of effects; therefore, the 

Project is not expected to affect surface waters during construction.

As previously discussed, soils are generally permeable in the study area. 

These soils would potentially allow for surface water and/or uncontrolled 

pollutant spills to infiltrate during construction, posing a risk to the sole 

source aquifer, critical aquifer recharge area, and wellhead protection area 

in this vicinity. However, implementation of required construction BMPs 

would avoid and minimize this risk; therefore, the Project is not expected 

to affect groundwater during construction.

How would the Project directly affect water resources after 

it is built?

Surface Waters

Effects to surface waters were evaluated in the context that the Project

would comply with applicable requirements of WSDOT’s NPDES 

Municipal Stormwater Permit64 and HRM standards,

65 as appropriate.

Flow Quantities

As previously discussed, the Project would construct new rail between 

South 66th Street at Rail MP 6.9 and 700 feet beyond the Lakewood 

Station at Rail MP 10.1. The Project would also remove and reconstruct 

the existing track between Rail MP 10.1 to the southern end of the Project. 

The new rail construction and existing rail reconstruction would

permanently remove approximately 24 acres of landscaped vegetation, 2.5 

acres of disturbed mixed forest, and one acre of scattered trees along the 

 64 Ecology 2009b. 65 WSDOT 2010b.
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Page 32 Water Resources Discipline Report

rail line right-of-way.

66 Track ballast material would also be added as part 

of the new construction and reconstruction. The ballast material would be 

permeable and would allow precipitation to continue to infiltrate. Stream 1 

crosses the project alignment in the area of new track construction, while 

Clover Creek, Stream 2, Murray Creek, and Stream 3 cross the project

alignment in the area of track reconstruction.

The Project would also implement roadway upgrades at Clover Creek 

Drive Southwest, N. Thorne Lane Southwest, Berkeley Street Southwest, 

41st Division Drive, and Barksdale Avenue. The surfaces added as part of 

the roadway improvements and associated sidewalk upgrades would be 

new impervious areas. The roadway upgrades would take place in the 

Clover Creek, Stream 2, and Murray Creek sub-basins.

Renovation of the Freighthouse Square station would utilize the existing 

structure and involve minor site development activities that would not 

result in significant changes to impervious surface quantities.

Removing vegetation in a watershed and/or adding impervious surface can 

change the hydrologic cycle by reducing infiltration, increasing the 

volume of surface runoff, and increasing the peak flow rate generated by a 

storm event.

67 Increased flows in streams can lead to scouring of the 

stream banks and changes in sediment transport patterns that can damage 

fish habitat. However, the land use changes expected under the Project

associated with the added track ballast, vegetation removal, and the new 

impervious surfaces would be below the HRM thresholds for flow control 

for each Project TDA.

As discussed, because the proposed changes in land cover would fall 

below the HRM thresholds for flow control, the Project is expected to 

comply with local, state, and federal water quality-based flow control 

standards without the use of additional flow control BMPs. In turn, the 

Project is not expected to affect water resources through changes in flow.

Water Quality

Removing vegetation in a watershed can result in surface erosion and 

sediment transport that increases turbidity, affects available oxygen 

supply, and affects habitat in receiving waters. Also, vehicle traffic 

associated with roadways and parking areas can produce metals, oil, and 

grease that are collected by surface water runoff and delivered to natural 

receiving waters. However, the amount of vegetation removal and 

pollution-generating area increases that would occur as part of the Project

for track construction and reconstruction, roadway upgrades, and the 

Freighthouse Square station renovations are expected to be below HRM

 66 WSDOT 2011b. 67 WSDOT 2010b.
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Water Resources Discipline Report Page 33

thresholds for water quality treatment requirements. Also, the Project

operation would not generate any pollutants identified on the Ecology 

303(d) list as concerns for surface waters within the study area. 

Under the presumptive approach outlined in the HRM, the Project is 

expected to comply with local, state, and federal water quality-based 

standards without the use of additional water quality BMPs and in turn is 

not expected to affect surface water quality.

Shorelines

The Project design would not significantly alter any areas within regulated 

shorelines; therefore, no effects are expected.

Floodplains

The Project design would not alter any of the water crossing structures in 

the Project right-of-way. In addition, the renovations at Freighthouse 

Square would be outside of any regulated floodplains. Therefore, the 

Project design would not affect jurisdictional flood zones, flood hazard 

areas, or base flood elevations.

Groundwater

Groundwater Supply

In addition to affecting surface waters as previously discussed, removing 

vegetation in a watershed and/or adding impervious surface can also 

reduce infiltration and associated groundwater recharge.68 However, the 

land use changes expected under the Project associated with the added 

track ballast, vegetation removal, and the new impervious surfaces would 

be below the HRM thresholds for flow control for each Project TDA. 

Therefore, the Project would allow precipitation to continue to infiltrate at 

levels similar to existing conditions and would not result in significant 

effects on groundwater recharge.

Water Quality

Metals, oil, and grease that are associated with roadways and parking 

areas can be collected by surface runoff and infiltrate into the ground. 

However, the amount of pollution-generating area increases that would 

occur as part of the Project for track construction and reconstruction, 

roadway upgrades, and the Freighthouse Square station renovations are 

expected to be below HRM thresholds for water quality treatment 

requirements. Finally, the Project operation would not generate any 

pollutants identified on the Ecology 303(d) list as concerns for surface 

 68 WSDOT 2010b.
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Page 34 Water Resources Discipline Report

waters within the study area. Therefore, no effects to groundwater quality 

are expected from the Project.

What potential indirect effects could occur from the 

Project?

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 Report69). Such 

redevelopment would be consistent with local zoning and approved by 

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

where surface waters are not present. Effects to surface and groundwater 

from redevelopment would be avoided through the use of required 

construction and design BMPs. Thus, no indirect effects to water resources 

are anticipated.

What cumulative effects would there be from the Project 

and other planned projects in the study area?

The Project would have no direct or indirect effect on water resources. 

Thus, the Project would not contribute to a cumulative effect on these 

resources.

Does the Project cause any significant unavoidable 

adverse effects?

As discussed above, risks to surface water and groundwater posed by the 

Project will be avoided through Project design and controlled through the 

use of construction BMPs; therefore, no direct or indirect adverse effects 

are expected. The risks of cumulative effects will similarly be controlled 

by each project in the area through compliance with applicable 

regulations. Therefore, no significant unavoidable adverse effects to water 

resources are expected from the Project.

 69 WSDOT 2012.
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Chapter 6 – Recommended 

Minimization Measures

What is considered “minimization?”

Minimization includes avoiding, minimizing, rectifying, reducing or 

eliminating, compensating, and/or monitoring project effects.70

What measures will be taken to minimize the effects during 

construction of the Project?

As discussed in Chapter 5, mitigation for potential construction-related 

water quality impacts would be addressed by complying with the NPDES

Construction Stormwater General Permit process,

71 and HRM standards

and BMPs,72 as appropriate.

Through compliance with the above requirements, an approved 

Construction Stormwater Pollution Prevention Plan (CSWPPP) would be 

developed and implemented for the proposed Project. The CSWPPP will

serve as the overall construction stormwater mitigation plan and will

include each of the following plans:

• Temporary Erosion and Sediment Control Plan

• Spill Prevention, Control, and Countermeasures Plan

• Concrete Containment and Disposal Plan

• Fugitive Dust Plan

Minimization contained in the CSWPPP aimed at preventing erosion from 

exposed soil will include the following:73

• The contractor will not leave disturbed areas exposed and 

unworked for more than seven days during the dry season 

(May 1-Sept. 30), or more than two days during the wet season 

(October 1 - April 30).

• Mulch, sodding, plastic covering, or other stabilization BMPs will

be used to prevent erosion in these areas.

 70 WSDOT 2010a. 71 Ecology 2010a. 72 WSDOT 2010b. 73 WSDOT 2007, Ecology 2010a.
September 2012 Point Defiance Bypass Project

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• Clearing will be limited to the footprint of the proposed cut.

• Water trucks will provide water as needed for dust control.

• The earthwork staging areas and equipment turnaround sites would 

be located in previously disturbed areas that support routine 

railroad access and maintenance activities as much as possible.

• The staging areas will not be located within 150 feet of a fishbearing or potentially fish-bearing water, or a water body that 

drains into fish-bearing waters.

• Silt fences and temporary sediment traps will be installed along 

critical areas.

• Site stabilization techniques will be implemented during 

construction, prior to the wet season, and for final site preparation.

• Disturbed areas will be permanently stabilized once construction is 

complete.

• All temporary and permanent erosion and sediment control BMPs 

will be maintained and repaired as needed to ensure continued 

performance.

BMPs contained in the CSWPPP aimed at preventing non-sedimentation 

pollutants, such as hazardous materials, from entering water bodies will

include the following:74

• All pollutants other than sediment that occur on site during 

construction will be handled and disposed of in a manner that does 

not contaminate stormwater.

• Staging areas for equipment repair and maintenance will be 

established away from all drainage courses.

• Washout from concrete trucks will be contained and covered when 

not in use to prevent it from entering storm drains or spilling onto 

soil or pavement that carries stormwater runoff.

• Thinners and solvents will not be used to wash oil, grease, or 

similar substances from heavy machinery or machine parts.

• A fuel truck will fuel equipment daily at the work sites, but this 

activity would be conducted a minimum of 150 feet away from 

surface water bodies and drainage conveyances.

• Fueling of construction vehicles and the storing of hazardous 

materials will not be conducted within 100 feet of any sensitive 

surface areas. 

• Any on-site fuel storage will have secondary containment equal to 

150 percent of storage capacity.

• Given the porous nature of the soils in the proposed Project area 

and the sensitive groundwater features, refueling and hazardous 

material storage would generally be conducted within contained 

areas.

 74 WSDOT 2007.
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The construction area will be designed to treat polluted runoff and 

contain spills.

How will operational effects be minimized?

As discussed in Chapter 5, control of potential risks to water resources 

will be addressed by complying with WSDOT’s NPDES Municipal 

Stormwater Permit75 and HRM guidance.

76 As a result, no effects to water 

resources are expected and no minimization is required.

 75 Ecology 2009b. 76 WSDOT 2010b.
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Ecology. 2009a. 2008 Washington State’s Water Quality Assessment 

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