Co

Water Quality Challenges in the San Francisco Bay/

Sacramento-San Joaquin Delta Estuary

United States

Environmental Protection

Agency

Unabridged Advance Notice of Proposed Rulemaking

February 2011

Cover Photo: Overlooking Middle River in the Bay Delta Estuary, taken by Chris Austin
Unabridged Advance Notice of Proposed Rulemaking for 

Water Quality Challenges in the San Francisco Bay/ 

Sacramento-San Joaquin Delta Estuary

February 2011

United States

Environmental Protection Agency
Summary

The U.S. Environmental Protection Agency (EPA) is publishing an advance notice of proposed 

rulemaking (ANPR) to seek comments from interested parties on possible EPA actions to 

address water quality conditions affecting aquatic resources in the San Francisco 

Bay/Sacramento-San Joaquin Delta Estuary (Bay Delta Estuary) in California. EPA is asking the 

public to consider broadly whether EPA should be taking new or different actions under its 

programs to address recent significant declines in multiple aquatic species in the Bay Delta 

Estuary. EPA is not limiting its request to actions that would require rulemaking. There may be 

a range of changes in EPA’s activities in the Bay Delta Estuary that would be constructive, 

including enforcement, research, revisions to water quality standards, etc. EPA will consider all 

comments before deciding what changes, if any, should be pursued. After reviewing the 

comments and completing its evaluation, EPA will provide the results of its review and any 

proposed next steps to the public. This ANPR identifies specific issues on which EPA solicits 

comment, including potential site-specific water quality standards and site-specific changes to 

pesticide regulation. In addition to the specific issues on which EPA solicits comments, EPA is 

interested in comments on any other aspects of EPA’s programs affecting Bay Delta Estuary 

aquatic resources. 

This ANPR has no regulatory impact or effect. The ANPR contains descriptions of certain EPA 

programs relevant to the Bay Delta Estuary and poses questions about how these programs could 

better protect and improve water quality for the benefit of aquatic resources in the Bay Delta 

Estuary. This ANPR marks the beginning of a process to consider possible changes to EPA 

programs in the Bay Delta Estuary. 

If EPA decides to pursue regulatory changes as a result of this ANPR, those regulatory changes 

will be made pursuant to appropriate formal rulemaking procedures. If changes to any 

regulations, rules, guidance or statutes are proposed and ultimately made final, to the extent such 

changes would require and/or authorize changes to state or tribal water quality standards or other 

regulations, states or authorized tribes would be affected. If changes to state or tribal regulations 

result from any final rule that EPA may promulgate in the future, entities subject to compliance 

with state or tribal regulations would also potentially be affected. For example, states and tribes 

authorized to implement the National Pollutant Discharge Elimination System (NPDES) Permit 

Program would need to ensure that permits they issue include any limitations on discharges 

necessary to comply with any water quality standards established as a result of any subsequent 

final rulemaking. Therefore, entities discharging pollutants to waters of the United States under 

NPDES could be affected by subsequent proposed and final rulemaking. 
Submitting Comments

Written comments must be received by EPA within 60 days of publication in the Federal 

Register.

Written comments may be submitted electronically at the Federal Rulemaking Portal 

(www.regulations.gov), identified by docket number EPA-R09-OW-2010-0976. Hard copy 

comments should be addressed to Erin Foresman, U.S. Environmental Protection Agency, 75 

Hawthorne Street, WTR-3, San Francisco, California 94105. 

All comments will be included in the public docket without change and will be made available 

online at www.regulations.gov, including any personal information provided, unless the 

comment includes Confidential Business Information (CBI) or other information whose 

disclosure is restricted by statute. Information that you consider CBI or otherwise protected 

should be clearly identified as such and should not be submitted through www.regulations.gov or 

e-mail. Regulations.gov is an ‘‘anonymous access’’ system and EPA will not know your identity 

or contact information unless you provide it in the body of your comment. If you send email 

directly to EPA, your e-mail address will be automatically captured and included as part of the 

public comment. If EPA cannot read your comment due to technical difficulties and cannot 

contact you for clarification, EPA may not be able to consider your comment. 

Docket: The index to the docket for this action is available electronically at www.regulations.gov 

and in hard copy at EPA Region 9, 75 Hawthorne Street, San Francisco, California. While all 

documents in the docket are listed in the index, some information may be publicly available only 

at the hard copy location (e.g., copyrighted material), and some may not be publicly available in 

either location (e.g., confidential business information). To inspect the hard copy materials, 

please schedule an appointment during normal business hours with Erin Foresman, 

foresman.erin@epa.gov; (916)557-5253.

For further information contact: Erin Foresman at U.S. Environmental Protection Agency, 

Region 9, Water Division, 75 Hawthorne Street, San Francisco, California 94105; 

foresman.erin@epa.gov; (916)557-5253.
Table of Contents

I. PURPOSE OF THIS ANPR....................................................................................................................1

II. INTRODUCTION TO EPA ACTIVITIES IN THE BAY DELTA ESTUARY ...................................5

A. Factual Background ...........................................................................................................................5

1. Current State of Estuarine Resources..........................................................................................5

2. Defining a Functional Estuary in a Changing Environment ....................................................10

B. EPA Programs in the Bay Delta Estuary..........................................................................................11

1. Clean Water Act.......................................................................................................................11

a. Water Quality Standards.............................................................................................11

b. Point Source Regulation .............................................................................................13

c. Total Maximum Daily Loads (TMDLs)......................................................................15

d. Nonpoint Source Management Program.....................................................................16

e. National Estuary Program...........................................................................................17

f. Wetlands Program .......................................................................................................17

g. State Water Quality Certification Program.................................................................18

2. Pesticide Regulation under the Clean Water Act and FIFRA..................................................18

III. PROGRAM AREAS FOR PUBLIC COMMENT .............................................................................20

A. Contaminants ...................................................................................................................................20

1. Request for Public Comment ..................................................................................................22

2. Ammonia: Toxic and Nutrient Effects.....................................................................................22

a. Aquatic Resource Issues .............................................................................................22

b. Regulatory Status........................................................................................................26

i. Water Quality Standards.................................................................................26

ii. Point Source Ammonia Discharges...............................................................27

iii. Nonpoint Source Ammonia Discharges.......................................................29

c. Request for Public Comment ......................................................................................29

3. Selenium ..................................................................................................................................30

a. Aquatic Resource Issues .............................................................................................30

b. Regulatory Status........................................................................................................31

i. Water Quality Standards.................................................................................31

ii. TMDLs and Implementation .........................................................................33
ii

c. Request for Public Comment ......................................................................................35

4. Pesticides .................................................................................................................................36

a. Aquatic Resource Issues .............................................................................................36

b. Regulation under FIFRA.............................................................................................40

c. Regulation under the Clean Water Act .......................................................................41

i. Water Quality Standards.................................................................................41

ii. TMDLs..........................................................................................................42

iii. Regulation of Agricultural Discharge...........................................................43

iv. Stormwater Permits ......................................................................................44

v. General NPDES Permits for Aquatic Pesticide Application .........................46

d. Request for Public Comment......................................................................................46

5. Contaminants of Emerging Concern........................................................................................48

a. Aquatic Resource Issues .............................................................................................48

b. Regulatory Status........................................................................................................49

c. Voluntary Activities....................................................................................................50

d. Request for Public Comment......................................................................................50

B. Protecting Estuarine Habitat, Fish Migration Corridors and Wetlands............................................52

1. Estuarine Habitat......................................................................................................................52

a. Aquatic Resource Issues .............................................................................................52

b. Regulatory Status........................................................................................................54

c. Request for Public Comment ......................................................................................56

2. Fish Migration Corridors .........................................................................................................57

a. Aquatic Resource Issues .............................................................................................57

b. Regulatory Status........................................................................................................59

c. Request for Public Comment ......................................................................................61

3. Wetlands ..................................................................................................................................62

a. Aquatic Resource Issues .............................................................................................62

b. Regulatory Status........................................................................................................62

c. Request for Public Comment ......................................................................................63

IV. EXECUTIVE ORDER 12866, Regulatory Planning and Review......................................................64

V. END NOTES ...................................................................................................................................... 65
ii

List of Selected Acronyms

ANPR Advance Notice of Proposed Rulemaking

AWQC Ambient Water Quality Criteria

BDCP Bay Delta Conservation Plan

C&D ELG Construction & Development Effluent Limitations Guideline and Standards

CA CGP California Construction General Permit

CA IGP California Industrial Stormwater General Permit

CBI Confidential Business Information

CCC California Coastal Commission

CDFG California Department of Fish and Game

CECs Contaminants of Emerging Concern

Corps U.S. Army Corps of Engineers

CVP Central Valley Project

CZARA Coastal Zone Act Reauthorization Amendments of 1990

DSC Delta Stewardship Council

DDT Dichlorodiphenyltrichloroethane

EDC Endocrine Disrupting Chemicals

EPA U.S. Environmental Protection Agency

ESA Endangered Species Act

FERC Federal Energy Regulatory Commission

FIFRA Federal Insecticide, Fungicide and Rodenticide Act

IEP Interagency Ecological Program

ILRP Irrigated Lands Regulatory Program

MAF Million Acre-Feet

MS4s Municipal Separate Storm Sewer Systems

NAS National Academy of Sciences

NCCP California Natural Community Conservation Plan Act

NMFS National Marine Fisheries Service

NPDES National Pollutant Discharge Elimination System 

NTR National Toxics Rule

NOAA National Oceanic and Atmospheric Administration

PGP Pesticides General Permit

POD Pelagic Organism Decline

POTW Publicly Owned Treatment Work

PPIC Public Policy Institute of California

RWQCB Regional Water Quality Control Board

SCCWRP Southern California Coastal Water Research Program

SDWA Safe Drinking Water Act

SFEP San Francisco Estuary Partnership

State Board California State Water Resources Control Board

SWP State Water Project 

TMDL Total Maximum Daily Load

USBR U.S. Bureau of Reclamation

USFWS U.S. Fish and Wildlife Service 

USGS U.S. Geological Survey

VAMP Vernalis Adaptive Management Plan

WQS Water Quality Standards

WPCF Water Pollution Control Facility

WWCF Wastewater Control Facility

WWTP Wastewater Treatment Plant

X2 Low Salinity Zone
1

I. PURPOSE OF THIS ANPR

The Bay Delta Estuary is a complex web of waterways, islands, and levees at the junction 

of the San Francisco Bay and the Sacramento and San Joaquin Rivers (see Figure A.)1 The Bay 

Delta Estuary is the hub of California's water distribution system, supplying some or all of the 

drinking water to 25 million people and irrigation water to 4 million acres of farmland. 

Water quality and aquatic resources in the Bay Delta Estuary are under serious stress. All 

of the waters of the Bay Delta Estuary and most of its tributaries are listed as impaired for one or 

more parameters under the federal Clean Water Act.2 Populations of many formerly abundant 

open-water (i.e., pelagic) fish species, including delta smelt, longfin smelt, and threadfin shad, 

have collapsed in recent decades. Anadromous3fishes, including the winter run chinook salmon, 

have suffered a similar decline. The decline of these aquatic resources has generated debate over 

water resource management in the Bay Delta Estuary. Delta interests, including state and federal 

agencies, environmental groups, urban and agricultural water users, commercial and recreational 

fishermen, and others have spent many years grappling with Bay Delta Estuary resource issues.

Concerns regarding Bay Delta Estuary water resource management increased during the 

2009 water year4as water users and resource managers struggled with the effects of three years 

of drought. Water export limitations caused by the drought and by restrictions imposed under 

the federal Endangered Species Act (ESA)5to assist struggling endangered species significantly 

reduced the availability of water for agricultural and urban uses.6 At the same time, the salmon 

fishery was closed on most of the West Coast for a second consecutive year as a result of 

declines in that fishery. Both the agricultural and fishery sectors suffered job losses as a result of 

the drought and the water export restrictions.

The federal government responded to this ongoing water management crisis with a broad 

set of actions.7 One of those actions was the creation of the Federal Bay Delta Leadership 

Committee, a Cabinet-level, multi-agency committee charged with coordinating federal 

responses to Bay Delta Estuary issues.8 The Federal Bay Delta Leadership Committee released 

its Interim Federal Action Plan for the California Bay-Delta (Federal Action Plan) on December 

22, 2009, outlining the federal government’s plan to address the Bay Delta Estuary and to work 

with the State of California to build a sustainable water future.9 The Federal Action Plan 

includes actions by EPA to “assess the effectiveness of the current regulatory mechanisms 

designed to protect water quality in the Delta and its tributaries, including standards for toxics, 

nutrients, and estuarine habitat protection.” EPA will also evaluate voluntary mechanisms that 

may be used to restore water quality in the Bay Delta Estuary. This ANPR is the beginning of 

this assessment. 

New scientific information about the Bay Delta Estuary and its aquatic resources has 

substantially increased in the past few years. This information has been developed and/or 

reviewed in reports10 synthesizing information on aquatic resources and water quality by the

following entities: the State/Federal Interagency Ecological Program Pelagic Organism Decline 

(POD) science team,

11 the State’s Delta Vision Blue Ribbon Task Force, the Public Policy 

Institute of California (PPIC), the U.S. Fish and Wildlife Service (USFWS) and National Marine 
2

Figure A. San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Bay Delta Estuary)
3

Fisheries Service (NMFS) as part of their biological opinions and associated independent science 

reviews, the California State Water Resources Control Board (State Board) and the Central 

Valley Regional Water Quality Control Board (Central Valley RWQCB).

12 Most of these 

studies and reports involve resources protected under the Clean Water Act and other EPA 

programs. 

EPA is using this ANPR to solicit and synthesize existing scientific information 

regarding the biological, chemical, and physical integrity of the Bay Delta Estuary’s aquatic 

resources. EPA will comprehensively review this information as it evaluates its statutory and 

regulatory options in the Bay Delta Estuary and will develop an appropriate response. 

Specifically, the purposes of this ANPR are:

(1) To review the current status of the EPA and Water Boards’13 responses to adverse 

water quality conditions that have been identified as potential contributors to the Bay 

Delta Estuary’s aquatic resources decline;

(2) To determine how best to implement existing programs under the Clean Water Act 

and the Federal Insecticide, Fungicide and Rodenticide Act (FIFRA)14 to improve Bay 

Delta Estuary water quality for aquatic resources; 

(3) To identify barriers, either programmatic or statutory, to improving Bay Delta Estuary 

water quality;

(4) To identify any additional scientific information regarding water quality related to 

aquatic resources in the Bay Delta Estuary; and

(5) To solicit input on whether EPA should be taking new or different actions under its 

programs to address aquatic resource problems in the Bay Delta Estuary.

Specific topics on which EPA is requesting comments appear in the sections below.

Related Efforts in the Bay Delta Estuary

There are several major efforts underway to address Bay Delta Estuary resources, 

including the regulatory programs of the Water Boards under state and federal water quality 

statutes. In July 2008, the Water Boards adopted a Strategic Workplan to coordinate and guide 

their Bay Delta Estuary activities.15 Over the next several years, these state activities will 

include, among others, multiple point source permit renewals, new pollutant and flow standards 

for the southern Delta and lower San Joaquin River, and Total Maximum Daily Loads (TMDLs) 

for pesticides in the Central Valley. EPA continues to support many of the elements in the 

State’s Workplan through technical and financial assistance.

Any EPA action taken as a result of this ANPR will complement the Water Boards’ 

actions, as EPA’s priority is to support and augment these efforts. As these efforts unfold, EPA

will monitor their progress and determine whether additional actions, consistent with its statutory 

authorities and responsibilities, are needed to ensure that the requirements of the Clean Water 
4

Act are satisfied. Finally, regardless of whether EPA pursues any new actions as a result of this 

ANPR, EPA believes the information gathered through the ANPR process may provide a factual 

basis for EPA’s ongoing activities under the Clean Water Act, the National Environmental 

Policy Act,16 and other federal statutes in the Bay Delta Estuary.

There are other federal and state water resource planning efforts underway in the Bay 

Delta Estuary. Stakeholders and relevant government agencies are engaged in developing the 

Bay Delta Conservation Plan (BDCP) under the federal ESA and the California Natural 

Community Conservation Plan Act (NCCP).17 The BDCP focuses on the recovery of ESA-listed

species and their habitat in the Bay Delta Estuary and is expected to include major proposals for 

changing how water is diverted and conveyed through the Bay Delta Estuary to the state and 

federal water export pumping facilities in the south Delta.

18

 The EPA’s responsibilities under 

the Clean Water Act to protect designated uses, such as estuarine habitat, fish migration, and 

threatened and endangered species, overlap with ESA requirements being addressed in the 

BDCP. Some actions taken pursuant to the BDCP will need to comply with both the ESA and 

Clean Water Act. To that end, EPA will ensure that any action it might take as a result of this 

ANPR will be closely coordinated with other federal and state actions related to the BDCP, any 

biological opinions on water operations affecting the Bay Delta Estuary, and any other actions 

requiring ESA compliance.

In addition, recent state legislation has established the Delta Stewardship Council (DSC), 

an independent state agency charged with developing a comprehensive resource management 

plan, the Delta Plan, by January 2012.19 The Delta Plan is intended to guide state and local 

agencies to help achieve the State's coequal goals of a reliable water supply and a restored Delta 

ecosystem. To inform the Delta Plan, the DSC’s Independent Science Board will evaluate the 

multiple stressors in the Bay Delta Estuary.20 Any EPA action taken as a result of this ANPR 

will also be coordinated with this and other related efforts.

The National Academy of Sciences (NAS) has initiated a review of some aspects of the 

science supporting ESA protections in the Bay Delta Estuary. Much of that scientific 

information is also relevant to Clean Water Act programs. Accordingly, EPA is coordinating 

with the NAS to assure that scientific evaluations serve the multiple regulatory programs in the 

Bay Delta Estuary.

Many activities discussed in this notice have been or are now the subject of a formal or 

informal rulemaking process conducted by either EPA or by a related state or federal agency. 

Nothing in this notice is intended to supersede those ongoing processes, nor does this notice 

constitute a decision under any of those processes. If commenters have submitted material in 

connection with those processes that is relevant to the issues raised in this notice, commenters

may either reference earlier submissions (if submitted to EPA), attach earlier submissions (if 

submitted to a different agency), or, if appropriate, provide a link to the material online.

Scope of this ANPR

This ANPR is focused on the most significant water quality factors adversely affecting 

aquatic species designated uses in the Bay Delta Estuary. Aquatic species, specifically the 
5

salmonids and pelagic species suffering significant population collapse during the last decade, 

brought the Bay Delta Estuary’s water resource management issues into sharp focus in recent 

years. EPA recognizes that the Bay Delta Estuary supports over 750 species of fish, mammals, 

birds, reptiles, amphibians, invertebrates, and plants, and that forty or more of these species are 

listed under state and/or federal endangered species laws.21 This ANPR is focused on aquatic 

species designated uses for waterbodies in the Bay Delta Estuary, but welcomes comment on 

how other species are being affected by water quality.

This ANPR does not comprehensively discuss water quality issues related to other 

designated uses, including drinking water, recreation, fish consumption, agriculture, etc. For 

example, water contact has been restricted in certain Bay Delta Estuary waters due to toxic bluegreen algae blooms. EPA acknowledges the ongoing need to evaluate and address these other 

issues.

Nothing in this ANPR constrains the discretion of the President or his successors to make 

whatever budgetary or legislative proposals he or his successors deem appropriate or desirable. 

The expenditure of any money or the performance of any obligation of the United States 

emanating from this ANPR shall be contingent upon appropriation or allotment of funds in 

accordance with 31 U.S.C. Section 1341 (Anti-Deficiency Act).22

II. INTRODUCTION TO EPA ACTIVITIES IN THE BAY DELTA ESTUARY

A. Factual Background

The Bay Delta Estuary is the intersection of two large river systems – the Sacramento and 

San Joaquin River basins – and a series of bays, marshes, and channels leading out to the San 

Francisco Bay and, ultimately, through the Golden Gate to the Pacific Ocean. Critical to 

California's social, political, economic and ecological well-being, the Bay Delta Estuary has long 

been the focus of competing interests (such as in-Delta agriculture, water exports, and flood 

control) that have significantly altered its waterways, flows, and adjacent lands. The Bay Delta 

Estuary is the hub of California's water distribution system, supplying drinking water to 25

million people and irrigation water to 4 million acres of farmland. Intensive urban and 

agricultural land uses in and upstream of the Bay Delta Estuary add an increasing and diverse 

array of water pollutants. As a result of these demands and stresses, the Bay Delta Estuary 

ecosystem, which is crucial habitat for many highly valued fish and wildlife species, has suffered 

greatly. Habitats are declining and fish populations have plummeted. Several species are listed 

as threatened or endangered under the ESA. Water quality in the Delta and its tributaries is 

impaired, contributing to the ecological and water supply crisis in the Bay Delta Estuary. The 

system is no longer a reliable source of high quality water for urban and agricultural use, 

especially in the quantities demanded in recent years. In addition, the Bay Delta Estuary’s 

outdated earthen levees face an unacceptably high risk of breaching.23

1. Current State of Estuarine Resources 

The decline of native fisheries in the Bay Delta Estuary over the past several decades is 

dramatic and well-documented.24 The graphs below summarize that decline since the 1970's, for 
6

migratory and resident fish.

25

The fall run of chinook salmon (Onchorhynchus tshawytscha) is the main run of salmon 

supporting the commercial and sport fisheries.26 Winter run and spring run chinook salmon are 

listed as endangered and threatened, respectively, under the ESA. Central Valley populations of 

green sturgeon (Acipenser transmontanus) and steelhead trout (Onchorhynchus mykiss) are also 

listed as threatened.

Figure B. Adult San Joaquin Salmon Returns 1960-2009

Commercial and sport fishing of salmon was cancelled by the Pacific Fishery 

Management Council for most of the western coast of North America in 2008 and 2009. A very 

limited season was authorized for 2010.27

The decline between 2007 and 2010 in the abundance of salmon appears to be due to 

poor ocean conditions leading to very poor ocean survival of one and two year old fish.28 

However, the sensitivity of the species to these ocean conditions is heightened by the long-term 

decline in freshwater and estuarine conditions, including pollution, diversion, and loss of shallow 

habitats.29 The loss of genetic diversity due to increased reliance on hatcheries has also 

contributed to reduced resilience of the fall run chinook salmon population. Impacts of the 2007-

2009 drought on the adult salmonid population are not yet measurable due to the time lag 

between spawning and maturation.

Many of the native and valued species of the upper Bay Delta Estuary are pelagic. 

Pelagic species live in open water, and are not usually associated with channel edges or physical 

structure. These species include two species (threadfin shad and striped bass) that were, until 

recently, the most abundant in the Bay Delta Estuary, as well as the ESA-listed delta and longfin 

smelt. 

After 2001, many of the pelagic species suffered nearly simultaneous, sharp population 
7

declines despite relatively favorable hydrological conditions. The declines occurred without the 

weather patterns usually associated with year-to-year variations in abundance and with no 

obvious other cause. Even in wetter periods, which historically have been associated with 

higher numbers, several of these species had record low abundances.30 The declining trends 

continued during the drought conditions of 2007-2009. Recent research indicates these declines 

represent an abrupt, significant drop in population abundance, rather than simply an extreme 

outcome of normal abundance cycles.31 

Figure C. Trends in four pelagic fishes from 1967 to 2009 based on the Fall Midwater Trawl32

0.0

0.3

0.6

0.9

1.2

1.5

1.8

66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 00 02 04 06 08 10

Abundance Index (Thousands)

Delta Smelt

Year

0

5

10

15

20

66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 00 02 04 06 08 10

Abundance Index (Thousands)

Striped Bass

Year
8

This sudden and unexpected decline (called the “Pelagic Organism Decline” or “POD”) 

has been intensively studied. The Interagency Ecological Program (IEP)33 began a number of 

investigations into likely causes of the decline including stock-recruitment, habitat degradation, 

increased predation or mortality at export facilities and changes in food web connections.34 All 

of these factors changed in nature or intensity around the time of the decline and have been 

implicated in the resilience and abundance of these fish populations. 

The government agency, academic, and stakeholder biologists studying the collapse of 

the pelagic and salmonid fisheries have identified several potential causes of the decline. These 

include:

0

2

4

6

8

10

12

14

16

66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 00 02 04 06 08 10

Abundance Index (Thousands)

Threadfin Shad

Year

0

2

4

6

8

10

12

14

16

18

20

66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 00 02 04 06 08 10

Abundance Index (Thousands)

Longfin Smelt

Year
9

(1) Water project operations. Sharp increases occurred in the number of fish trapped by and

collected at the State Water Project (SWP) and Central Valley Project (CVP) export facilities at 

the same time that catches in all other collection programs declined and water exports out of the 

Bay Delta Estuary consistently increased.35 After 2001, approximately 6 million acre-feet 

(MAF) of new water storage space became available south of the Delta. The availability of this 

new storage space enabled approximately 1 MAF of additional annual exports from 2001 

through 2006. Total annual exports went from a maximum of about 5 MAF in the late 1990s to 

about 6 MAF in 2001-2007. Since that time, exports have dropped back down due to drought 

and ESA restrictions, but threatened and endangered fish populations have continued to stay at 

extremely low levels. Existing regulatory standards are oriented toward export restrictions in the 

spring to protect critical migration periods during high flow months. The 1 MAF of additional 

annual exports were generally taken during the fall and early winter months. The increased 

exports taken between 2001-2007 resulted in (1) greater levels of entrainment36 and (2) 

reductions in Delta outflow and a parallel decline in the volume of estuarine habitat (measured 

by the areal extent of low salinity zones) for several species (delta smelt, striped bass, and 

threadfin shad) in the fall of those years.

37

(2) Invasive Species. Invasive overbite clams have established year-round populations in the 

western Delta and are implicated in the reduction in abundance of both diatoms and zooplankton 

that are the base of the food web for pelagic fish.

38

 At the same time, invasive jellyfish have 

become a large part of the pelagic environment and are known to compete with small fish for 

food and to prey directly on young fish. Further, the composition of the base of the food web has 

shifted to smaller and less nutritious invasive species.

(3) Ocean conditions. Ocean conditions (including limited ocean food sources and adverse 

temperature conditions) during the drought played a large part in the recent declines of 

anadromous fish, and upstream and migratory conditions made the populations less resilient to 

such oceanic stressors.39 Ocean conditions alone appear to have little effect on the declining 

resident Delta fishes.40

(4) Contaminants. The contribution of water pollution, or contaminants, to the instability of the 

Bay Delta Estuary aquatic ecosystem and the specific role of contaminants in the decline of 

pelagic fishes has been examined in the past decade. Pyrethroid insecticide41 use became much 

more common after the year 2000 and may be associated with tissue abnormalities found in delta 

smelt and striped bass.42 Some pyrethroid insecticides are toxic to aquatic invertebrates, food for 

pelagic fishes, at very low levels.43 In-Delta discharges from Delta islands are a source of 

contaminants to the Bay Delta Estuary. The composition of discharge from these Delta islands is 

largely uncharacterized; it consists primarily of irrigation return flow, levee seepage, and 

precipitation runoff.

Other contaminants are also present in the Bay Delta Estuary,44 sometimes at toxic 

levels.45 Ammonia/um discharges from the Sacramento and Stockton wastewater treatment 

plants led to loadings that could be expected to affect algal community composition and 

growth.46 Although the Stockton plant converted to more effective levels of treatment in 2007, 

the Sacramento plant has continued to generate ammonia/um at levels that have prompted

intensive examination of downstream impacts, particularly reductions in the growth of diatoms 
10

(which are the base of the food web for most pelagic fish). Chemical treatment of estuarine 

waters to combat the spread of submerged aquatic weeds began in 2002.47 Summertime blooms 

of the toxic blue-green algae Microcystis aeruginosa became more widespread throughout the 

decade, extending downstream to the habitat usually occupied by delta smelt and young striped 

bass in 2007. Blue-green algal growth and blooms have been linked to ammonia loadings and 

herbicide treatments such as those used to treat aquatic weeds.

48

Current research findings do not support the idea that a “single stressor” is responsible for 

the ecological changes in the Bay Delta Estuary.49 Most research supports the idea of multiple 

stressors, interacting in concert, as the cause of the Bay Delta Estuary ecosystem decline. Most 

efforts at synthesizing Bay Delta Estuary research have converged on a vision of an ecosystem 

that is shifting its species composition in response to a suite of changes in flow, nutrients, 

contaminants, temperature and turbidity.50

2. Defining a Functional Estuary in a Changing Environment

Research efforts that began as a response to the POD have identified several significant 

and fundamental changes in the physical nature of the Bay Delta Estuary: water temperatures and 

water clarity have been increasing; nitrogen loading has been increasing while phosphorus 

loading has been decreasing, resulting in substantial changes in nutrient ratios; and water exports 

have been substantially increasing while outflows to the San Francisco Bay have been low and 

stable for much of the year. Simultaneously, the ecological community of the upper Bay Delta 

Estuary appears to have shifted from a food web based on diatoms, large copepods, and pelagic 

fish to one of cyanobacteria, jellyfish, clams, and emergent vegetation housing large populations 

of the predatory largemouth bass and their relatives. Species which prefer the shallow edges of 

riverbeds, such as non-native sunfish, bass, and minnows that live among invasive submerged 

vegetation, have become dominant. This change is associated with habitat shifts, as introduced 

vegetative coverage has increased each year.51 The aquatic resources of the Bay Delta Estuary 

seem to be shifting from the former pelagic, estuarine community to an assemblage of invasive 

species more characteristic of a eutrophic stable system, including harmful algal blooms, 

jellyfish, clams, and freshwater fishes.52

Many, if not most, of these fundamental changes in Bay Delta Estuary ecology are the 

result of human activities over the past century or more: 800 million cubic yards of gold rush 

mining debris; the reclamation of delta islands for human use; the dredging, deepening and 

channelization of waterways; the export of significant amounts of water; the introduction of 

undesirable invasive species; and the introduction and the increase of a wide range of 

contaminants into the Bay Delta Estuary’s waterways.53 Equally significant additional changes 

affecting the Bay Delta Estuary will challenge resource managers in the future. The antiquated 

levee system - a system that has suffered at least 160 major levee failures over the past century54

- will face new stresses from continued subsidence, seismic events, and climate change-induced 

rise in sea levels.55 The pattern and nature of precipitation is also anticipated to change, as less 

snow and more rain present additional challenges for the flood control system in the Bay Delta 

Estuary and for water resource managers. Changes in precipitation and runoff patterns, 

combined with warmer air temperatures, will continue to raise water temperatures. 56 
11

Given these current and probable future changes in the Bay Delta Estuary, the challenge

for California and federal regulatory agencies and water resource managers is to align regulatory 

programs and public investments to enable the Bay Delta Estuary to achieve all of its desired 

uses.

B. EPA Programs in the Bay Delta Estuary 

Two federal statutes under EPA jurisdiction are important to Bay Delta Estuary aquatic 

resource issues. The most relevant is the federal Clean Water Act, which establishes standards 

for protecting the nation’s water resources and establishes implementation approaches for point 

source discharges and nonpoint sources of pollution.57 Under the Clean Water Act, EPA is 

authorized to delegate many Clean Water Act programs to requesting qualified states and tribes. 

In California, most of the Clean Water Act programs have been formally delegated to the State, 

with EPA retaining an oversight role and, in some cases, a mandatory review and approval role.

In addition to the Clean Water Act, the Federal Insecticide, Fungicide, and Rodenticide 

Act, 7 U.S.C. Sections 136 et seq. (FIFRA) governs pesticide use nationally and prescribes 

restrictions on the use of pesticides to assure reasonable certainty of no harm to aquatic species 

in the Bay Delta Estuary, taking into account the economic, social, and environmental costs and 

benefits of the pesticide use. Under FIFRA, EPA has accorded primary enforcement 

responsibility for pesticide use violations (primacy) to California, with EPA providing funding 

and technical assistance.

1. Clean Water Act

There are several regulatory components of the Clean Water Act that affect Bay Delta 

Estuary issues: water quality standards under Section 303(c) , point source discharge regulation 

under the National Pollution Discharge Elimination System (NPDES) program under Section 

402, the listing of impaired waters with responsive Total Maximum Daily Load (TMDL) 

calculations under Section 303(d), nonpoint source management programs under Section 319, 

and the wetlands regulatory program under Section 404. EPA also provides annual grants to 

California to carry out Clean Water Act programs, including the programs under Sections 106 

and 319. In 2010 alone, these grant programs provided more than $22 million to programs in 

California. In addition, each year EPA provides California with two large capitalization grants, 

one under the Clean Water Act and another under the Safe Drinking Water Act (SDWA). These 

funds are added to California’s revolving loan programs which provide low-interest financing for 

a range of water quality and environmental improvement projects. Since 2008, EPA has 

awarded California $942 million through these two grant programs. In addition, through the 

National Estuary Program under Section 320, EPA provides additional funding to the San 

Francisco Estuary Partnership (as described below).

a. Water Quality Standards 

Water quality standards (WQS) serve as the foundation for the water-quality based 

approach to pollution control and are a fundamental component of watershed management. 

Section 303(c) of the Clean Water Act establishes the basis for the current water quality 
12

standards program. That section:

1. Defines water quality standards;58

2. Identifies acceptable designated uses: public water supply, propagation of fish and 

wildlife, recreational purposes, agricultural and industrial water supplies and navigation;

3. Requires that state and tribal standards protect public health or welfare, enhance the 

quality of water and serve the purposes of the Act;59

4. Requires that states and tribes review their standards every three years; and

5. Establishes the process for EPA review and approval of state and tribal standards, 

including, where necessary, the promulgation of a superseding federal rule in cases where 

a state's or tribe's standards are not consistent with applicable requirements of the Clean 

Water Act or in situations where the Administrator determines that federal standards are 

necessary to meet the requirements of the Act.

Generally, states establish water quality standards on a watershed or broader basis, but 

they can also address unique aquatic circumstances through the use of site-specific standards. 

These site-specific standards can apply to a single waterbody or a particular segment of a 

waterbody, where hydrological or other factors make a broadly-applicable standard 

unacceptable.

Water quality standards for the Bay Delta Estuary waters are contained in three separate 

water quality control plans: (1) the State Board’s 2006 Water Quality Control Plan for the San 

Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 WQCP), (2) Central Valley 

RWQCB’s 2009 Sacramento River and San Joaquin River Water Quality Control Plan and (3) 

San Francisco Bay RWQCB’s 2007 Water Quality Control Plan for the San Francisco Bay 

Basin. These plans contain water quality standards for the Bay Delta Estuary, including 

designated uses and water quality criteria. The State Board’s 2006 WQCP is the final authority 

with respect to any overlap between the Regional Water Boards’ water quality control plans. 

Collectively, these water quality control plans identify designated uses for Bay Delta Estuary

waters that include: municipal, domestic, industrial, and agricultural water supply, groundwater 

recharge, navigation, water recreation, fishing, warm and coldwater habitat, migration habitat, 

spawning and reproduction habitat, wildlife, estuarine, and rare, threatened and endangered 

species habitat. 

Narrative and numeric water quality criteria are established in each of the three water 

quality control plans to protect designated uses. The State Board’s 2006 WQCP establishes flow 

criteria while the Regional Boards’ plans contain contaminant criteria.60 The 2006 WQCP 

protects fish and wildlife designated uses with ten water quality criteria focused on controlling 

levels of salinity, dissolved oxygen, and flow characteristics (volume, frequency, duration, 

timing, and direction of flow). The majority of criteria set numeric limits for the allowable 

amounts of pollutants (e.g., salinity or dissolved oxygen) or establish flow restrictions or 

characteristics that must be met at specific locations and times throughout the Delta based on the 
13

type of water year.61 The Regional Boards’ plans use narrative criteria for broad categories such 

as toxicity and use numeric criteria for specific contaminants such as chlorpyrifos and ammonia.

b. Point Source Regulation 

The Clean Water Act requires EPA (or, in the case of delegated states such as California, 

the State) to control point source discharges through the issuance of NPDES permits, which may 

be issued for fixed terms that may not exceed five years.62 EPA has issued comprehensive 

regulations that implement the NPDES program at 40 CFR part 122. The Clean Water Act also 

provides for the development of technology-based and water quality-based effluent limitations 

that are imposed through NPDES permits to control the discharge of pollutants from point 

sources.63

The Clean Water Act directs EPA to promulgate effluent limitations guidelines and 

standards (effluent guidelines) that reflect pollutant reductions that can be achieved by categories 

or subcategories of industrial point sources using technologies that represent the appropriate 

level of control.64 For point sources that introduce pollutants directly into the waters of the 

United States (direct dischargers), the effluent limitations guidelines and standards promulgated 

by EPA are implemented through NPDES permits.65 For sources that discharge to Publicly 

Owned Treatment Works (POTWs) (indirect dischargers), EPA promulgates pretreatment 

standards that apply directly to those sources and are enforced by POTWs and state and federal 

authorities.66

Two particular types of point source discharges are of particular interest in the Bay Delta 

Estuary. First, discharges from POTWs have been identified as possible contributors to 

impairments in the Bay Delta Estuary. There are ten POTWs discharging into the Bay Delta 

Estuary with a discharge capacity of 10 million gallons/day or more.67 In recent years, the Water 

Boards have been updating and, generally, strengthening effluent discharge restrictions in some 

of the NPDES permits.68 For example, the renewal of the City of Stockton’s Waste Water 

Treatment Plant NPDES permit in 200269 and subsequent Cease and Desist Order70 required a 

wastewater treatment plant upgrade including nitrification facilities to meet effluent restrictions 

on ammonia/ammonium discharges and protect downstream designated uses.

The second type of discharge particularly relevant in the Bay Delta Estuary is stormwater 

discharge. In 1987 Congress amended the Clean Water Act, adding section 402(p) which created 

a phased approach to the regulation of stormwater discharges under the Clean Water Act. EPA’s 

Phase I stormwater regulations in 1990 established requirements for medium (serving between 

100,000 and 250,000 people) and large (serving 250,000 people) municipal separate storm sewer 

systems (MS4s) and discharges associated with industrial activity.71 In its 1999 Phase II 

stormwater regulations, EPA designated discharges associated with small construction activity 

and discharges from small MS4s (less than 100,000 people and located within an urbanized area 

defined by the Bureau of the Census) for regulation under the Clean Water Act.72 In certain 

situations, a stormwater discharge may be more appropriately and effectively regulated by an 

individual permit, a region-specific general permit, or by inclusion in an existing Phase I permit. 

Thus, under current EPA regulations, there are three general categories of stormwater discharges 

that are directly regulated by EPA and California under the Clean Water Act: discharges from 
14

MS4s, discharges associated with construction activity, and discharges associated with industrial 

activity.73 In California, permits for discharges of stormwater are issued by the Regional Water 

Boards or the State Board.

Discharges from MS4s: An “MS4” is a conveyance or system of conveyances (including 

roads with drainage systems, municipal streets, catch basins, curbs, gutters, ditches, man-made 

channels, or storm drains): (i) owned or operated by a public body; (ii) designed or used for 

collecting or conveying stormwater; (iii) which is not a combined sewer; and (iv) which is not 

part of a Publicly Owned Treatment Works (POTW).74 In California, large and medium MS4s 

obtain individual NPDES permits from the Regional Water Boards. The Central Valley 

RWQCB issues permits to the majority of the stormwater discharges from MS4s to the Bay 

Delta Estuary and its tributaries. Small MS4s include systems similar to general municipal storm 

sewer systems, such as systems at military bases, large hospital or prison complexes, and 

highways and other thoroughfares, but do not include separate storm sewers in very discrete 

areas, such as individual buildings.75 In 2003, the State Board adopted a statewide general 

permit for discharges from small MS4s.76 

Stormwater Discharges Associated with Construction Activity: Discharges associated 

with “large” construction activity includes those discharges associated with clearing, grading,

and excavation of five acres or greater of total land area.

77

 Discharges associated with “small” 

construction activity includes those discharges associated with clearing, grading and excavation 

that results in land disturbance of equal to or greater than one acre and less than five acres.78 In 

California, stormwater discharges from construction sites are permitted by individual NPDES 

permits issued by the Regional Boards or the California Construction General Permit79 issued by 

the State Board. 

Stormwater Discharges Associated with Industrial Activity: Discharges associated with 

industrial activity include those from any conveyance that is used for collecting and conveying 

stormwater and that is directly related to manufacturing, processing or raw materials storage 

areas at an industrial plant as laid out at 40 C.F.R. 122.26(b)(14)(i)-(x). In California, 

stormwater discharges associated with industrial activity are permitted by individual NPDES 

permits issued by the Regional Boards or the California Industrial Stormwater General Permit 

(97-03-DWQ) issued by the State Board. 

In addition to the above three general categories of stormwater discharges subject to 

regulation, both EPA and California have the authority to require NPDES permits for additional 

stormwater discharges that are currently not directly regulated under the Clean Water Act by 

using their residual designation authority. EPA and/or California may require a permit for an 

unregulated stormwater discharge if it determines that either (1) stormwater controls are needed 

for the discharge based on waste load allocations that are part of total maximum daily loads that 

address the pollutant(s) of concern; or (2) the discharge or category of discharges within a 

geographic area contributes to a violation of a water quality standard or is a significant 

contributor of pollutants to waters of the United States.80 Additionally, EPA or California may 

designate small MS4s whose discharges are currently unregulated for NPDES permit coverage.81
15

c. Total Maximum Daily Loads 

Regulation of point sources is not always sufficient to attain ambient water quality 

standards in all waterbodies. Clean Water Act Section 303(d)(1)(A) requires each state to 

identify and prioritize those waters where technology-based controls are inadequate to attain 

WQS:

Each State shall identify those waters within its boundaries for which the effluent 

limitations required by section 1311(b)(1)(A) and section 1311(b)(1)(B) of this title are 

not stringent enough to implement any water quality standards applicable to such waters. 

The State shall establish a priority ranking of such waters, taking into account the 

severity of the pollution and the uses to be made of such waters.82

The state’s identification of such impaired waters constitutes the “303(d) list.”83 States have 

been required, since 1992, to submit their 303(d) lists to EPA for review and approval every two 

years.

84.

 If it disapproves a state’s list, EPA must establish a list for the state.85

For all waters identified under Section 303(d)(1)(A) as exceeding water quality 

standards, the Act provides:

Each State shall establish for the waters identified in paragraph (1)(A) of this subsection, 

and in accordance with the priority ranking, the total maximum daily load, for those 

pollutants which the Administrator identifies under section 1314(a)(2) of this title as 

suitable for such calculation. Such load shall be established at a level necessary to 

implement the applicable water quality standards with seasonal variations and a margin 

of safety which takes into account any lack of knowledge concerning the relationship 

between effluent limitations and water quality.86

The term “total maximum daily load” (TMDL) is not explicitly defined in the Clean Water Act. 

EPA’s current regulations define a TMDL for a pollutant as the sum of the “wasteload 

allocations” allocated to point sources, the “load allocations” allocated to nonpoint sources or 

natural background, and a margin of safety.87 Therefore, a TMDL identifies the maximum 

amount of a pollutant that can be added to a waterbody (loading capacity) without exceeding 

water quality standards.88

States must establish TMDLs for waters where pollutants are “preventing or expected to 

prevent attainment of water quality standards.”89 Under Section 303(d)(2), EPA is required to 

review and approve or disapprove TMDLs established by states for listed waters.90 In its review, 

EPA takes into consideration the legal and technical adequacy of the TMDL, which includes 

elements identified above and an implementation schedule. If it disapproves a state TMDL, 

EPA must establish the TMDL.91 Implementation is the responsibility of states. In California, 

the Porter-Cologne Water Quality Control Act requires that a TMDL include an implementation 

plan.

TMDLs established pursuant to Section 303(d)(1) for impaired waters are not selfexecuting. Limitations in loadings identified for point sources (waste load allocations) are 
16

enforced through permits issued pursuant to Section 402 of the Act.92 Limitations in loadings 

identified for nonpoint sources (i.e., “load allocations”), on the other hand, may only be 

“required” under state law.93

All of the waters within the Bay Delta Estuary are listed as impaired by at least one 

factor, either due to the presence of pollutants at unacceptable levels or the lack of maintaining 

certain conditions such as adequate levels of dissolved oxygen. The State Board revised and 

adopted a new 303(d) list in August 2010 and submitted that list to EPA for its review and 

approval. On November 12, 2010, EPA partially approved and partially disapproved 

California’s list, adding additional water bodies and pollutants.94

In California, TMDLs are developed by the Regional Boards but are not final until 

approved by the State Board and EPA. EPA has approved TMDLs for salinity, boron, mercury, 

selenium, diazinon, chlorpyrifos, pathogens and low dissolved oxygen to address impairments 

affecting the Delta. The Central Valley RWQCB is developing a salinity TMDL for the San 

Joaquin River upstream of Vernalis, as well as a pesticides TMDL for the Central Valley.95

d. Nonpoint Source Management Program

Nonpoint source pollution – pollution caused by a wide range of activities including 

urban development, agriculture and forestry – is a major cause of water quality impairment 

nationally and in California. Two primary federal statutes establish a framework in California 

for addressing nonpoint source water pollution: Section 319 of the Clean Water Act and Section 

6217 of the Coastal Zone Act Reauthorization Amendments of 1990 (CZARA). Together these 

statutes require the state to assess water quality problems associated with nonpoint source 

pollution and to develop programs to address these challenging problems. EPA oversees these 

nonpoint source programs and provides funding to the state for program implementation.

California’s Porter-Cologne Water Quality Control Act designates the Water Boards as 

the state agencies with primary responsibility for water quality control in California and 

obligates them to address all discharges of waste that could affect the quality of the waters of the 

state, including potential nonpoint sources of pollution. The Porter-Cologne Water Quality 

Control Act’s scope and implementation authorities are significantly broader than those found in 

the federal Clean Water Act. In addition to using the Porter-Cologne Water Quality Control 

Act’s planning, permitting, and enforcement authorities to prevent and control nonpoint sources 

of pollution, the Water Boards have implemented a program of outreach, education, technical 

assistance and financial incentives. 

California submitted an "upgraded" nonpoint source pollution control program to EPA 

and the National Oceanic and Atmospheric Administration (NOAA) on February 4, 2000. The 

Plan for California's Nonpoint Source Pollution Control Program (Program Plan) was jointly 

submitted by the State Board and the California Coastal Commission (CCC) to satisfy the 

requirements of the Clean Water Act Section 319 and CZARA Section 6217. NOAA and EPA 

found that California satisfied all conditions of program approval pursuant to CZARA Section 

6217, set forth in the Findings on the California Coastal Nonpoint Program, transmitted to the 

State on July 17, 2000. Furthermore, EPA found that the Program Plan successfully incorporates 

the nine key elements pursuant to Clean Water Act Section 319, which characterize an effective 
17

and dynamic state nonpoint source program. The California Nonpoint Source Pollution Control 

Program was fully approved pursuant to CZARA Section 6217 and Clean Water Act Section 

319. As a result, California has continued to receive at least $10 million from EPA annually to 

implement the nonpoint source program. 

e. National Estuary Program (NEP)

The San Francisco Estuary Partnership (SFEP) was established in 1987 under the 

National Estuary Program pursuant to Clean Water Act Section 320. The purpose of each of the 

28 designated NEPs is to collaboratively develop and implement an EPA-approved 

Comprehensive Conservation and Management Plan (CCMP) for the protection of local 

estuarine resources. Nationally, NEP structures provide for broad stakeholder involvement. 

SFEP’s structure includes an Executive Council, a Steering Committee and an Implementation 

Committee to provide strategic direction to the Director and program staff. The CCMP’s 

geographic scope encompasses 60,000 acres of watershed drainage to the San Francisco Bay and 

Delta. SFEP recently developed a strategic plan to direct resources to wetland and watershed 

restoration, water quality improvements through green infrastructure, and climate change 

readiness, with most activities focused on the nine Bay Area counties. SFEP oversees and tracks 

implementation of the CCMP (as completed in 1993 and revised in 2007), manages research and 

restoration projects, and educates the public about Bay Delta Estuary issues including wetlands, 

wildlife, aquatic resources and land use. SFEP is funded through an array of federal, state, and 

local grants and contracts. EPA provides annual funding to each NEP. In 2010, EPA provided 

SFEP with $800,000.

f. Wetlands Program 

Section 404 of the Clean Water Act regulates the discharge of dredged and fill materials 

into waters of the United States.

96

 Activities regulated under Clean Water Act Section 404 

include discharging fill material (e.g., dirt) into waters for urban development, water resource 

projects (dams, levees, canals, and pipelines), infrastructure (utilities, roads, airports), and 

mining (in-stream gravel mining, tailings discharge from mountaintop coal mining). Section 404 

requires a permit to be issued before dredged or fill material may be discharged into waters of

the United States. 

Clean Water Act Section 404 protects water quality by restricting the destruction (fill) of 

aquatic resources that maintain and improve water quality and serve other important functions.97 

Clean Water Act Section 404 prohibits granting a permit for the discharge of fill material into 

waters of the United States when there is a practicable alternative that is less damaging to the 

aquatic environment and when the proposed discharge would significantly degrade aquatic or 

other natural resources.98 EPA promulgated the Section 404(b)(1) Guidelines to implement these 

basic concepts.

Administration of Clean Water Act Section 404 is divided between the U.S. Army Corps 

of Engineers (Corps) and EPA. The Corps administers the permitting program by processing 

individual and general permits, determining Clean Water Act jurisdiction, and conducting 

compliance assistance. The Corps writes regulations and develops national and district policies. 
18

EPA is responsible for oversight, including writing regulations that must be followed in issuing 

404 permits, developing policy and guidance, determining the scope of geographic jurisdiction, 

reviewing and commenting on individual permit applications, conducting enforcement actions 

against unpermitted fill activities, and, where appropriate, objecting to or vetoing individual 404 

permits. 

Fill activities that destroy wetlands and other slow-moving waterways are relevant to 

water quality, in that wetlands, sloughs, mudflats, floodplains, and similar aquatic resources 

perform water filtration services that reduce common types of water pollution, like excessive 

nutrients, sediment, municipal sewage, pesticides, and toxicity events. Wetlands, sloughs, and 

floodplains are flat areas where water moves slowly, allowing sediment to drop out of the water 

column and deposit on the bottom. Nutrients and other contaminants from pesticide and 

fertilizer application, animal waste, septic tanks, stormwater and municipal sewage are often 

absorbed by plant roots and microorganisms in the soil while other pollutants stick to sediment 

particles.99 Wetlands can be so effective at removing pollutant loads that artificial wetlands are 

occasionally constructed to treat stormwater and wastewater. 

Wetlands, sloughs and floodplains also provide important floodwater storage and aquatic 

habitat services, by absorbing flood waters in times of high precipitation and slowly releasing 

them back into the larger tributary system. This important service not only mitigates the 

economic damage of floods, it improves the quality of flood waters by allowing pollutants to 

settle out and be processed by vegetation and/or sediment microorganisms. These aquatic 

resources also provide necessary spawning, forage, and refuge habitat for fish and wildlife. 

Clean Water Act Section 404 protects these services by limiting the discharge of dredged and fill 

material and the subsequent destruction of wetlands. 

g. State Water Quality Certification Program 

The Clean Water Act Section 401 water quality certification program provides states with 

an opportunity to address aquatic resource impacts from federally issued permits and licenses. 

Section 401 restricts federal agencies from issuing a permit or license for any activity that may 

result in a discharge to waters of the United States from a point source until the state certifies that 

the proposed discharges do not violate water quality protection provisions. States have several 

options under the Clean Water Act Section 401 program. They can (1) grant certification, (2) 

grant certification with conditions, (3) deny certification, or (4) waive the requirement for 

certification. In California, the federal licenses and permits most frequently requiring Section 

401 certification include Clean Water Act Section 404 permits, Federal Energy Regulatory 

Commission (FERC) hydropower licenses, and Rivers and Harbors Act Section 9 and 10 permits 

issued by the Corps.

2. Pesticide Regulation under the Clean Water Act and FIFRA

Pesticides are being discussed separately in this notice because they are regulated under 

at least two major statutes that take different approaches to regulation. First, some pesticides are 

classified as pollutants pursuant to the Clean Water Act, and, as such, are subject to the Clean 

Water Act programs outlined above (water quality standards, NPDES permits, TMDLs, nonpoint 
19

source management programs, etc.) 

Pesticides are also regulated under Federal Insecticide, Fungicide and Rodenticide Act 

(FIFRA). Under FIFRA Section 3, every pesticide product must be registered with EPA or 

specifically exempted under FIFRA Section 25(b) before being sold or distributed in the United 

States. An applicant for a new registration or an existing registrant (collectively referred to as 

applicant here) must demonstrate to EPA’s satisfaction that, among other things, the pesticide 

product, when used in accordance with widespread and commonly recognized practice, will not 

cause ‘‘unreasonable adverse effects’’ to humans or the environment. This safety determination 

requires EPA to weigh the risks of the use of the pesticide against any benefits. EPA must 

determine that the standard for registration contained in FIFRA is met before granting a 

registration. The three primary action points for EPA under FIFRA are registration, 

reregistration, and registration review.

1. Registration. Section 3 of FIFRA contains the requirements for registration. FIFRA Section 

3(c)(2) provides EPA broad authority, before and after registration, to require scientific testing 

and submission of the resulting data to EPA by applicants for registration of pesticide products. 

An applicant must furnish EPA with data on the pesticide, its composition, toxicity, potential 

human exposure, environmental properties, and ecological effects, as well as information on its 

product performance (efficacy) in certain cases. Although the data requirements are imposed 

primarily as a part of initial registration, EPA is authorized under FIFRA Section 3(c)(2)(B) to 

require a registrant to develop and submit additional data to maintain a registration.

2. Reregistration. FIFRA Section 4 requires that EPA reregister each pesticide product first 

registered before November 1984. This date was chosen because pesticides registered before 

then, were not subject to the more stringent 1984 regulation review process. EPA has completed 

the reregistration/tolerance reassessment process for food use pesticides and expects to complete 

all reregistration activities by 2014. 

3. Registration review. FIFRA section 3(g) mandates that all pesticide registrations are to be 

periodically reviewed. Changes in science, public policy, and pesticide use practices occur over 

time. Through the new registration review program implemented via a regulation promulgated 

in 2006,100 EPA periodically reevaluates all registered pesticides to assure that they continue to 

meet the statutory standard of “no unreasonable adverse effects.” Starting in 2006, registration 

review began to replace EPA’s reregistration program as the mechanism for systematic review of 

existing pesticides.

A major component of the FIFRA program for protecting sensitive species is the reliance 

on pesticide container labeling to disseminate use restrictions. In addition to label instructions 

physically attached to pesticide containers, users are required to comply with geographically 

specific use limitations, if any, that are reflected in EPA’s Endangered Species Protection 

Bulletins. Users are required to follow label and Bulletin instructions or they are subject to 

enforcement actions under the misuse provisions of FIFRA. 

As discussed in detail below, pesticide registration for pesticides affecting Bay Delta 

Estuary aquatic resources has been the subject of intensive review and litigation in recent years.
20

III. PROGRAM AREAS FOR PUBLIC COMMENT

In this ANPR, EPA is asking the public to consider broadly whether EPA should take

new or different actions under its programs to address problems in the Bay Delta Estuary. EPA 

is not limiting its request to actions that would require actual rulemaking; there may be a range 

of changes in EPA’s activities in the Bay Delta Estuary that would be constructive, including 

enforcement, research, revisions to water quality standards, etc. Any change in EPA activities 

would be dependent on existing authority and the availability of existing or new resources. Any 

changes requiring EPA rulemaking would provide for public comment through the notice and 

comment rulemaking process. 

A substantial amount of research was performed and evaluated in connection with the 

scientific review of the pelagic organism decline. As noted above, that process identified a 

number of potential stressors affecting the Bay Delta Estuary aquatic ecosystem. Many of those 

potential stressors are directly or indirectly affected by the EPA programs described above. EPA 

has identified certain topics for more focused consideration in this ANPR. These are:

- Ammonia

- Selenium

- Pesticides

- Contaminants of Emerging Concern

- Estuarine Habitat 

- Fish Migration Corridors

- Wetlands 

EPA has not made any attempt to rank these topics as to their importance in resolving 

Bay Delta Estuary issues.101 EPA’s preliminary evaluation suggests that each of these topics, if 

addressed, could contribute to a resolution of Bay Delta Estuary resource conflicts. While this 

ANPR discusses these topics separately, EPA is mindful that the more significant concern is the 

cumulative and interactive effects of multiple stressors on the Bay Delta Estuary’s aquatic 

resources.

Commenters may also identify additional topics that impact Bay Delta Estuary resource 

management, if EPA has some programmatic involvement in the topic.

A. Contaminants

Poor water quality in the Bay Delta Estuary and its tributaries affects terrestrial and 

aquatic ecosystems, drinking water, recreation, industry, agriculture, and the local, state, and 

interstate economy. The State of California collects data on contaminants that degrade water 

quality to generate its Clean Water Act Section 303(d) list of water bodies with designated use 

impairments. All Bay Delta Estuary waters are impaired due to many different contaminants, 

including pesticides, manufacturing compounds, metals (including selenium), pathogens, 

nutrients/low dissolved oxygen, invasive species, salinity, and toxicity from unknown sources.102 

Some pesticides and metals are legacy problems, such as the banned organochlorine pesticide 

DDT and mercury from abandoned mines. Most contaminants contributing to poor water quality 
21

in the Bay Delta Estuary are the result of current-use compounds from industrial, agricultural, 

urban, transportation, and natural sources. In addition, there is growing concern about new 

classes of contaminants, such as pyrethroid pesticides, pharmaceuticals and personal care 

products.

Contaminant “toxicity” refers to effects ranging from death to behavioral abnormalities 

or other impairments to growth, reproduction and survival.103 Numeric water quality criteria are 

usually identified for individual chemicals as concentrations that protect designated uses from 

toxicity due to short-term (acute) exposure and longer-term (chronic) exposure. In recent years, 

more attention has turned to the potential for contaminants, individually or in combination in the 

aquatic environment, to produce “sub-lethal” effects (e.g., glycogen depletion, cellular stress, 

impaired swimming ability, reduced reproductive success) that can lead to declining populations 

in sensitive species.

It is difficult to evaluate and address contaminants in the Bay Delta Estuary in the 

absence of a comprehensive water quality monitoring program. Some contaminants are 

monitored only on an incidental or occasional basis, or not at all. Consistent monitoring data 

over any particular time period is unavailable. Monitoring data is collected by multiple agencies, 

with little standardization of monitoring procedures, data quality assurance or presentation 

protocols, and is not readily accessible in any single database. This makes data interpretation 

difficult. EPA is working with the Water Boards and other partners to develop a comprehensive 

Regional Monitoring Program to address these problems.

Contaminants are considered one of the contributing factors in the abrupt drop in pelagic 

organisms. The IEP’s Pelagic Organism Decline science review is investigating how individual 

contaminants affect pelagic species. Initial studies have somewhat conflicting conclusions. One 

study evaluated historic monitoring data of contaminants and Bay Delta Estuary organism 

population estimates and concluded that direct toxicity to POD species from contaminants in Bay 

Delta Estuary waters is unlikely to be the cause of the recent large population declines. That 

study also concluded, however, that contaminants cannot be ruled out as a major contributor to 

the POD due to the potential for direct toxicity to POD food sources and gaps in monitoring data 

that prevent a more complete evaluation.104 Another study used statistical methods to evaluate 

the relationships between the POD and various hypothesized causes such as contaminants and 

water exports out of the Bay Delta Estuary. This statistical analysis suggested that contaminant 

loadings of ammonia and ammonium to the Bay Delta Estuary are more highly correlated with 

the POD than water exports over a 30-year period.105 Other important studies show high levels 

of toxicity to aquatic invertebrates from urban stormwater pyrethroid pesticide loadings to Bay 

Delta Estuary tributaries106 and sub-lethal, population-level impacts to sport fish from the 

mixture of contaminants in Bay Delta Estuary waters.107

The existing research indicates that contaminants are likely contributors to the POD and 

ecosystem collapse. It is a complex task to determine which of the contaminants in the Bay 

Delta Estuary are individually, or in combination with one another, or under specific physical 

conditions, responsible for the POD and current state of the Bay Delta Estuary aquatic 

ecosystem. A list of contaminants has emerged as potentially significant, including ammonia 

and ammonium, selenium, and pesticides. Another group of contaminants, usually containing 
22

some hormonally-active ingredients, are considered “contaminants of emerging concern” 

(CECs). The following sections examine these contaminants with respect to impacts to Bay 

Delta Estuary aquatic resources and source control provided by the current regulatory 

framework.

1. Request for Public Comment

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information with citations that support your comments.

2. Ammonia: Toxic and Nutrient Effects

a. Aquatic Resource Issues 

Background

Total ammonia nitrogen in aquatic systems is both a toxic substance and a source of 

nutrients for aquatic plants, depending on its form. Ammonia is a chemical compound 

containing nitrogen that exists in two forms in water, un-ionized ammonia (NH3) gas and 

dissolved ionized ammonium (NH4+).108 This document will use the term un-ionized ammonia 

to refer to ammonia gas (NH3), ammonium to refer to the ammonium ion (NH4+) and total 

1. Are there contaminants, other than those named above, causing adverse impacts to 

aquatic resource designated uses in the Bay Delta Estuary and that should receive more 

focused review? 

2. How can pollutant-specific water quality criteria effectively address or incorporate 

interactive effects between multiple contaminants and other physical, chemical, and 

biological stressors?

3. What methods can be used in developing and implementing TMDLs to effectively 

address or incorporate interactive effects between multiple contaminants and other physical, 

chemical, and biological stressors on individual water bodies or for water bodies within a 

watershed?

4. What information exists about how climate change impacts will affect contaminant 

pollution (generally or for individual contaminants)?
23

ammonia nitrogen to refer to the combination of ammonia and ammonium. Un-ionized ammonia 

gas is toxic to vertebrates109 and ammonium is a source of nitrogen, a necessary nutrient, for 

aquatic plants. Total ammonia nitrogen is the term used to inclusively refer to both un-ionized 

ammonia gas and ammonium and their collective impacts.

Total ammonia nitrogen toxicity is primarily a function of pH but also depends on 

temperature and salinity. Total ammonia nitrogen is toxic to all forms of aquatic life.110 Unionized ammonia is considerably more toxic to vertebrates than ammonium; toxicity increases 

with pH as the proportion of un-ionized ammonia to ammonium increases. Toxicity decreases 

with pH as the proportion of ammonium rises. Nevertheless, ammonium makes a relevant 

contribution to total ammonia nitrogen toxicity. Toxic effects of total ammonia nitrogen exist at 

lower pH111 and some aquatic invertebrates may be more sensitive to ammonium than to unionized ammonia.112

 

Un-ionized ammonia is especially harmful to vertebrates in aquatic environments where 

ambient total ammonia nitrogen levels can become concentrated. High levels of un-ionized 

ammonia gas in water reverse the diffusive gradient of un-ionized ammonia movement out of 

cells, leading to a rise of ammonia gas in the blood stream, which causes cell death in the central 

nervous system, convulsions, coma and death.113 Non-lethal impacts of ammonia gas on fish 

include swelling and thickening of gills, respiratory and oxidative stress, and increased 

occurrences of gill disease from parasites and harmful bacteria.114

Around the country, excessive total ammonia nitrogen is a water pollution problem 

because it is a source of nitrogen. Although some amount of nitrogen is necessary for plant 

growth, elevated amounts can inhibit plant growth. Excessive nitrogen stimulates harmful 

blooms of some types of algae (phytoplankton), which in turn reduce dissolved oxygen during 

algae decomposition and can lead to die-offs of aquatic animals. Elevated levels of ammonium 

are also known to inhibit growth of some types of desirable estuarine phytoplankton such as 

diatoms. These conditions reduce ecosystem biodiversity and stability after prolonged periods. 

Harmful algal blooms also cause taste and odor problems in drinking water and cause respiratory 

distress and neurological problems in human recreational users.115 

One unique characteristic of the Bay Delta Estuary is that it has both excessive nutrient 

loadings and low phytoplankton primary productivity. The Bay Delta Estuary is one of the least 

productive tidal estuaries in the world. Between the late 1970's and 1990's phytoplankton 

biomass and photosynthetic productivity declined 60% and 40% respectively.116 Ammonium 

loadings to the Bay Delta Estuary have increased since the 1980's and may be one reason why 

phytoplankton biomass and productivity have decreased. Excessive nutrients are often 

associated with high primary productivity and algal blooms. In the Bay Delta Estuary, however, 

nutrient (ammonium) concentrations are high enough to inhibit growth of diatoms, important 

algae in the food web.

117

Total ammonia nitrogen sources in the Bay Delta Estuary include wastewater treatment 

plants and agricultural and urban runoff containing ammonium fertilizers and animal waste. The 

largest total ammonia nitrogen point sources affecting the Bay Delta Estuary are wastewater 

treatment plants.118
24

Total Ammonia Nitrogen and the Decline of Bay Delta Estuary Pelagic Organisms 

Total ammonia nitrogen discharges to the Bay Delta Estuary are one of the potential 

contributors to the long-term decline and recent collapse of pelagic organism populations and the 

Bay Delta Estuary food web. The relationship between total ammonia nitrogen levels and 

plunging fish populations is being actively investigated by the U.S. Geological Survey (USGS), 

the State Board, the Central Valley RWQCB, the Interagency Ecological Program, academic 

research groups, and some water supply agencies. Collectively, these research efforts suggest 

that total ammonia nitrogen concentrations in the Bay Delta Estuary may be contributing to the 

decline in pelagic fishes through one or more of the following mechanisms: (1) direct toxicity to 

pelagic fishes; (2) toxicity to pelagic organism food sources; (3) increased toxicity to pelagic 

organisms in the presence of other contaminants or physical conditions; and/or (4) by 

contributing to trophic (ecosystem) food web changes that negatively impact resource 

availability for pelagic species.119

Total ammonia nitrogen levels observed in the Bay Delta Estuary may be directly toxic to 

pelagic species, such as delta smelt, and their food sources. Increases in total ammonia nitrogen 

loadings to the Bay Delta Estuary are correlated with decreases in fish120 and copepod 

populations;121 however, the relative contribution of total ammonia nitrogen versus other 

variables (hydrologic modification, water exports, invasive species, other contaminants) to the 

pelagic organism decline is unclear. 

Completed toxicity investigations on delta smelt suggest that ambient total ammonia 

nitrogen concentrations present in the Bay Delta Estuary do not cause acute toxicity in delta 

smelt.122 Chronic toxicity conditions for delta smelt potentially exist when pH is greater than 

8.0;123 however, the Central Valley RWQCB reports that pH levels in the Delta do not often 

exceed 8.0.124

Ambient total ammonia nitrogen levels in the Bay Delta Estuary may be contributing to 

acute and chronic toxicity in copepods, an important pelagic fish food source. Ten percent 

mortality was observed in copepods at ambient Bay Delta Estuary concentrations, indicating the 

potential for acute total ammonia nitrogen toxicity.125 Preliminary experimental data show a 

negative effect on copepod reproduction and survival rates at ambient ammonia concentrations 

commonly observed in the Bay Delta Estuary.126

The toxic effect of total ammonia nitrogen on pelagic species and food sources may occur 

at lower concentrations than established toxicity endpoints when present with other contaminants 

or due to differences between toxicity testing and exposure in natural environments. Multipollutant experiments show that copepods may be considerably more sensitive to total ammonia 

nitrogen concentrations in the presence of copper and pesticides.127 Methods for establishing 

toxicity end points use delta smelt larvae reared in hatcheries that may be healthier and less 

vulnerable to pollutant exposures than delta smelt larvae reared in the Bay Delta Estuary exposed 

to a mixture of pollutants from the start of their life cycle. Similarly, toxicity identification 

experiments for individual species generally use non-swimming fish even though there is 

evidence that swimming, unfed fish may be several times more sensitive to ambient ammonia 

levels than laboratory exposures.128
25

Abundant nitrogen from increased ammonium discharges into Bay Delta Estuary waters 

may be a significant variable contributing to changes that negatively impact the food supply for 

pelagic organisms. The Bay Delta Estuary is characterized by some of the lowest photosynthetic 

(primary) productivity by phytoplankton in tidal systems globally. Phytoplankton productivity is 

the food supply for higher trophic level pelagic organisms. Ammonium loadings and other 

stressors to the Bay Delta Estuary have increased since the 1980's while phytoplankton biomass 

and productivity have decreased. Ammonium concentrations that inhibit phytoplankton growth 

rates are frequently present in the Bay Delta Estuary

129 along with multiple other stressors, such 

as high filtering rates from introduced clams, hydromodification, and presence of other 

contaminants that affect food web biomass and composition.130

The phytoplankton community in the Bay Delta Estuary has changed from one dominated 

by diatoms to one dominated by blue-green algae and flagellate phytoplankton species.131 

Diatoms were the primary food item for the calanoid copepod Eurytemora affinis, an important 

food source for pelagic fish.132 Copepods prefer diatoms over blue-green algae and flagellates133

potentially because diatoms are more nutritious, containing greater amounts highly unsaturated 

fatty acids than blue-green algae,134 and calanoid copepods cannot capture small particles such as

nutritionally rich nanoflagellates.135

The long-term decrease in phytoplankton biomass coupled with the change from a 

diatom-dominated community to blue-green algae and flagellate-dominated community 

represents a reduction in quality and quantity at the base of the food web that may affect fish 

populations. Diatoms are food for copepods; copepods are food for forage fish and other pelagic 

species; forage fish are food for both native and non-native fish species. As diatom biomass 

declined, so did some populations of copepods and crustaceans.

Increased loadings of total ammonia nitrogen to the Bay Delta, along with other 

variables, may contribute to the reduction of pelagic food sources and subsequently pelagic fish 

populations by supporting the growth of blue-green algae and suppressing growth of diatoms. 

Long-term population declines of Bay Delta Estuary pelagic fishes are correlated with long-term 

increases in wastewater effluent and ammonium loadings to Bay Delta Estuary waters.136 

Flagellates and blue-green algae may out-compete diatoms by preferentially using nitrogen in the 

form of ammonium,137 while diatoms more easily use nitrogen in the form of nitrate.138 Ambient 

ammonium levels in the Bay Delta Estuary inhibit diatom uptake of nitrate, suppress diatom 

growth, and prevent spring time diatom blooms that support higher trophic level pelagic 

species.139 Phytoplankton composition and declining pelagic fish populations are also correlated 

with Bay Delta Estuary flows and water temperature.140 

A recent important change in the Bay Delta Estuary food web composition is the increase 

in abundance of toxic blue-green algae, Microcystis aeurginosa (Microcystis). Blooms of 

Microcystis were first observed in 1999 and have quickly spread throughout the central and 

southern Delta. Microcystis exists as an algae layer on the water surface that impairs recreation 

activities, reduces dissolved oxygen, causes taste and odor problems in drinking water and 

toxicity problems in fish. Microcystin, the toxin produced by Microcystis, promotes tumors in 

fish, has been measured in phytoplankton, zooplankton, and fish tissue in the Bay Delta Estuary, 

and may be negatively impacting the health of striped bass and other Bay Delta Estuary fish.141 
26

Estuarine fisheries may be impacted by Microcystis through direct toxicity from microcystin 

and/or indirectly through food web impacts from degraded nutritional value. Microcystis blooms 

are occurring with increasing frequency in the Bay Delta Estuary.

142

 Some data show positive 

correlations between ammonia loadings to the Bay Delta Estuary and Microcystis abundance and 

distribution.143 However, other research shows that high water temperature and stream flow has a 

stronger relationship with Microcystis cell density than nutrient loadings to the Bay Delta 

Estuary.144

b. Regulatory Status

i. Water Quality Standards

Water Quality Control Plans are written by the Water Boards and contain the state and 

region’s applicable water quality standards, which are composed of designated uses and narrative 

or numeric criteria for regulated pollutants. Neither the State Board nor the Central Valley 

RWQCB has adopted narrative or numeric criteria specifically for total ammonia nitrogen, unionized ammonia or ammonium. They do, however, contain narrative toxicity criteria that 

prohibit concentrations of toxic substances that cause acute or chronic toxicity to aquatic life. 

The San Francisco RWQCB adopted numeric criteria for un-ionized ammonia concentrations 

(0.025 mg/L annual median) but the San Francisco Bay Water Quality Control Plan does not 

have numeric or narrative criteria for total ammonia nitrogen or ammonium.145 

EPA publishes and periodically updates its recommended aquatic life water quality 

criteria to reflect the latest scientific knowledge. These criteria are a guide for states, territories, 

and tribes to develop water quality standards and a foundation for controlling discharges of total 

ammonia nitrogen into waterways. The 1999 EPA Aquatic Life Ambient Water Quality Criteria 

for Ammonia – the most recent final recommended criteria for ammonia – identifies the chronic 

limit for total ammonia nitrogen as 1.3 mg/L (measured by milligrams of nitrogen per liter of 

water at pH 8.0 and temperature 25 degrees Celsius).146 The acute limit is 5.6 mg/L under the 

same test conditions. 147 Monitoring data indicate that Sacramento River and Bay Delta Estuary 

total ammonia nitrogen concentrations are below the 1999 EPA-recommended numeric water 

quality criteria for ammonia.148 

Recent independent investigations in the Bay Delta Estuary raise the possibility that the 

1999 EPA ammonia criteria may not be protective of pelagic species in the Bay Delta Estuary. 

The lethal concentration of total ammonia nitrogen for two copepod species, Eurytemora affinis

and Psuedodiaptomus forbesi (an important pelagic fish food sources) occurs at or below the 

calculated 1999 EPA ammonia criteria, and the estimated chronic criterion concentration for 

these copepods is below the 1999 EPA chronic ammonia criteria.149 A study at the University of 

California concluded that the chronic 1999 EPA ammonia criteria may not be protective of delta 

smelt because the lethal concentration of un-ionized ammonia for delta smelt is approaching the 

chronic criteria at high pH (8.3).150 This study may not be conclusive in the Bay Delta Estuary 

because the Central Valley RWQCB found that pH values above 8.0 are rare in the Sacramento 

River downstream of the Sacramento Regional Wastewater Treatment Plant (WWTP).

151

EPA proposed to update the recommended Ammonia Aquatic Life Criteria on December 

20, 2009. The proposed acute limit is 2.0 mg/L (25 degrees Celsius, pH 8.0, mussels present); 
27

the proposed chronic limit is 0.26 mg/L (25 degrees Celsius, pH 8.0, mussels present.)152 Once 

final, the updated EPA criteria are not effective in California until the Water Boards adopt them 

as a change to their Basin Plans, the Water Boards use the updated criteria in effluent limitations 

in permits for point source discharges, or the EPA promulgates the updated criteria as a water 

quality standard for California. 

It is unclear whether total ammonia nitrogen levels in the Bay Delta Estuary would meet 

or exceed the proposed 2009 Ammonia Aquatic Life Criteria. A Central Valley RWQCB field 

study shows that ambient ammonia concentrations measured in the Bay Delta Estuary between 

March 2009 and February 2010 did not exceed the proposed 2009 chronic ammonia criteria.153

Contrary information submitted to the Central Valley RWQCB suggests that total ammonia 

nitrogen concentrations immediately outside of the Sacramento Regional WWTP mixing zone 

would have exceeded the proposed 2009 criteria 21 per cent of the time between 2007 and 2008 

and 41 per cent of the time in 2009.154

ii. Point Source Ammonia Discharges

Regulating point source discharges of total ammonia nitrogen is a major component of 

the water quality regulatory approach in the Bay Delta Estuary. The Water Boards directly 

control point sources of total ammonia nitrogen through ammonia effluent limits in NPDES 

permits. In the absence of numeric ammonia criteria, these permits are generally designed to 

meet the narrative toxicity criteria. NPDES permit limits for ammonia are site-specific and are 

based on the 1999 EPA Aquatic Life Ambient Water Quality Criteria for Ammonia, the narrative 

toxicity criteria, effluent ammonia concentrations from the discharge source, concentration of 

total ammonia nitrogen in the receiving water body, and available dilution.

The major ammonia point sources affecting the Bay Delta Estuary are publicly owned 

treatment works (POTWs). The table below shows the permit status of these facilities. The two 

largest POTWs discharging treated sewage to the Bay Delta Estuary are the Sacramento 

Regional WWTP and the Stockton Regional Wastewater Control Facility (WWCF). Sacramento 

Regional WWTP is the largest wastewater discharge in the Bay Delta Estuary with an average 

dry design flow of 181 million gallons per day. The Sacramento Regional WWTP is the greatest 

source of ammonia/ammonium loading to the Bay Delta Estuary, discharging approximately 14 

tons of ammonia/ammonium per day to the Sacramento River.155 

The Central Valley RWQCB recently issued a new NPDES permit to the Sacramento

Regional WWTP changing the ammonia effluent limits and requiring tertiary treatment and 

nitrogen removal.

156
28

1. Effluent limit at ph 8.0, T 26 deg C with salmonids present 

2. Effluent limit at pH 7.1, T 22 deg 30 day average/

3. Effluent limit seasonal 0.75 mg/L 1 May – 31 Oct, 1.11 1 Nov – 30 April.

Major Ammonia NPDES Discharges in and near Delta157

Facility Name 

Permit 

Expiration 

Date NPDES Permit

Discharge 

Design Flow 

(million 

gallons/day)

Treatment 

Level 

Secondary (S) 

or Tertiary (T)

Ammonia 

Effluent 

Limit

(mg/L)

Sacramento Regional Wastewater 

Treatment Plant (WWTP) 8/1/2005 R5-2000-0811 181 S none

Stockton Regional Wastewater 

Control Facility (WWCF) 12/23/2014 R5-2008-0154 55 T 5

Central Contra Costa Sanitation 

District WWTP 3/31/2012 R2-2007-0008 53.8 S none

Fairfield-Suisun WWTP 5/31/2014 R2-2009-0039 17.5 S 2

Vallejo Sanitary Flood Control District 

WWTP 9/30/2011 R2-2006-0056 15.5 S none

Easterly WWTP 4/1/2013 R5-2008-0055 15 S 1.3

City of Woodland Water Pollution 

Control Facility (WPCF) 3/27/2009 R5-2009-0010 10.4 T 0.8

City of Manteca WPCF 10/1/2014 R5-2009-0095 9.9 T 1.4

Tracy WWTP 5/1/2014 R5-2008-0086 9 S 1.3

City of Lodi, White Slough WPCF 9/1/2012 R5-2007-0133 7 T 1.3

Mountain House WWTP 5/1/2012 R5-2007-0039 5.4 T 1

Brentwood WWTP 12/31/2012 R5-2008-0087 5 T 0.8

City of Benicia WWTP 3/1/2008 R2-2008-0014 4.5 S 35

Ironhouse Sanitary District WWTF 4/1/2013 R5-2008-0057 4.3 T 1.1

UC Davis Main WWTP 12/1/2013 R5-2008-0183 3.6 T 0.753

Mt. View Sanitary District WWTP 5/17/2010 R2-2006-0063 3.2 S 8

City of Galt WWTP 1/1/2009 R5-2004-0001 3 T 3.52

Discovery Bay WWTP 11/30/2013 R5-2008-0179 2.1 S 4.641
29

The Stockton Regional WWCF discharges have an average dry design flow of 55 million 

gallons/day, approximately one third the size of the Sacramento RWTP. The Stockton Regional 

WWCF was upgraded to include treatment processes that remove ammonia because it could not 

meet the ammonia effluent limits established in its 2002 NPDES permit.158 The upgraded 

Stockton Regional WWCF is operating and significantly reducing ammonia in the treated 

effluent.159

iii. Nonpoint Source Ammonia Discharges

Potential nonpoint source discharges of total ammonia nitrogen into the Bay Delta 

Estuary include runoff from livestock waste, onsite waste water treatment systems (septic tanks) 

and runoff containing agricultural and urban fertilizer. There is limited information available 

about the volume of nonpoint sources of ammonia in the Bay Delta Estuary. A recent evaluation 

of nutrient loading to the Bay Delta Estuary by the Central Valley RWQCB suggests that the 

Sacramento Regional WWTP is the primary source of nitrogen to the Bay Delta Estuary

downstream of the effluent discharge point from March 2009 to February 2010.160 This 

suggests a limited contribution of total ammonia nitrogen from nonpoint sources.

c. Request for Public Comment

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information with citations that support your comments.

1. What, if any, information is available on the sources or impacts of total ammonia nitrogen 

in the Bay Delta Estuary that is not reflected or cited above?

2. Is there any information available that suggests site-specific water quality standards for 

total ammonia nitrogen in the Bay Delta Estuary may be more effective than current 

standards due to unique hydrological, chemical, biological, or physical conditions? 

3. What information is needed to determine effective site-specific water quality standards for 

total ammonia nitrogen, including narrative or numeric criteria?

4. What information is available on nonpoint sources of total ammonia nitrogen and how 

they may most effectively and efficiently be controlled?
30

3. Selenium

a. Aquatic Resource Issues

Selenium is a naturally occurring element that, when mobilized in the environment and 

transformed to organic, bioavailable forms, is highly bioaccumulative.161 Although selenium is a 

micronutrient, it is highly dose-sensitive and can be toxic to organisms at very low levels of 

chronic exposure.162 Selenium toxicity in fish and wildlife reduces reproductive success through 

effects that lower embryo survival, such as deformed growth (teratogenesis).163 In California, 

the damaging consequences of toxic levels of selenium first came to public attention in the 1980s 

when deformed waterfowl were discovered at Kesterson Reservoir in the San Joaquin Valley. 

Subsequent research has substantially advanced understanding of selenium sources and 

mobilization in the Bay Delta Estuary, the processes through which selenium enters and builds 

up in the ecosystem, and the effects of selenium on different species. In particular, this science 

points to the role of site-specific conditions, such as hydrology, geochemistry, food web, and 

species characteristics in determining risk to aquatic life and wildlife.164 The new information 

raises significant questions as to whether the existing regulatory regime adequately protects 

aquatic life and wildlife.165

Selenium is naturally present in certain soils of marine origin and can enter the 

environment when precipitation introduces the selenium-bearing deposit to water. 

Environmental problems with selenium typically occur when large amounts are mobilized 

through human activities such as irrigation, mining or processing of organic fuels. Once 

converted to an actively bioavailable form, selenium tends to stay in a bioavailable form – a 

characteristic that contributes to build up in the environment over time.166 Selenium has several 

dissolved forms (notably selenate, selenite and organo-selenide) that differ in transformation 

rates and bioavailability. The least bioavailable form, selenate, can be reduced by organisms to 

selenite and then incorporated into cells as organo-selenium. 

Aquatic food webs can be particularly efficient in taking up selenium and transferring it 

up the food web. At the base of the food web, microorganisms such as bacteria and algae take in 

and assimilate selenium from ambient water. Since biotic exposure to selenium occurs through 

diet, rates of exposure are affected by concentrations in species’ food sources. Some prey 

species bioaccumulate selenium more efficiently than others. For example, Corbula amurensis, 

an introduced clam that occurs from San Pablo Bay through Suisun Bay and Marsh and the 

central and southern Delta, accumulates selenium at roughly three times the rate of supplanted 

native clam species.167 As a result, predator species that feed on Corbula, such as diving ducks 

(scaups and scoters) and white sturgeon, suffer high exposure to bioaccumulated selenium. In 

contrast to the Delta-dwelling white sturgeon, green sturgeon are more sensitive to selenium but 

spend less time in the Bay and Delta waters; compared to white sturgeon, green sturgeon spend 

more time in marine waters and also upstream of the Delta in the Sacramento River.168 In 

addition to duration of exposure, timing of exposure relative to sensitive life stages can be a 

factor in impacts. For example, concerns have been expressed about the possibility that juvenile 

salmon, which use the Delta and San Joaquin River, might be sensitive to selenium.169

Biological variables, such as species sensitivity to selenium and preferred habitat and 
31

diet, are among the reasons that water column concentration of selenium is not in itself a reliable 

indicator of exposure. Differences in hydrologic conditions and associated water chemistry also 

affect the degree to which selenium accumulates at a given site. Where waters are relatively still 

and flushing is limited (lentic systems), conditions promote build-up of the more bioavailable 

forms of selenium such as selenite. In flowing rivers or streams (lotic systems) both the flushing 

function of flows and the typical form of selenium (selenates) limit uptake. 

The main controllable sources of selenium in the Bay Delta Estuary are agricultural 

drainage (generated by irrigation of seleniferous soils in the western side of the San Joaquin 

basin) and discharges from North Bay refineries (in processing selenium-rich crude oil from the 

southern San Joaquin Basin). Both the San Joaquin River and North Bay selenium loads have 

declined in the last 15 years in response to, first, a control program in the San Joaquin Grasslands 

area, and, second, NPDES permit requirements established for refineries in the late 1990s.170 

The annual loads of selenium (mostly as selenate) entering the Bay Delta Estuary from the San 

Joaquin and Sacramento rivers vary by water year (that is, by flow), but dissolved selenium 

loadings averaged 2,380 kg/year from the San Joaquin and 1,630 kg/year from the Sacramento in 

the 1990-2007 period.171 The Sacramento River selenium concentration, however, is essentially 

at background levels (.06 +/- .02 micrograms/L), without evidence of significant controllable 

sources. 

Pollutant loading, transport, and residence time in the Bay Delta Estuary could change 

appreciably as a result of actions that are under consideration or being implemented. These 

actions include increases in San Joaquin River flows to restore the river and salmon runs, 

changes in water supply conveyance and related channel flow in the Bay Delta Estuary, and 

habitat restoration projects within the Bay Delta Estuary. San Joaquin River restoration or other 

flow augmentation programs could change the capacity of flows to mobilize and transport 

selenium-rich water and suspended sediments into the Bay Delta Estuary. Within the Bay Delta 

Estuary, exposure to selenium could increase in planned restoration habitats such as wetlands 

and floodplains. Thus, while the actions may have beneficial ecosystem and/or water supply 

objectives, there is some risk of exacerbating the impacts of selenium unless corrective measures 

are taken.

b. Regulatory Status

i. Water Quality Standards

EPA promulgated ambient water quality criteria for selenium in the Bay Delta Estuary 

and watershed through the National Toxics Rule (NTR) in 1992. The National Toxics Rule 

values are reiterated in the California Toxics Rule, issued by EPA in 2000.172 Subsequently, the 

California Toxics Rule and Water Boards’ Basin Plan amendments have established consistent 

values for aquatic life. The applicable chronic aquatic life criterion (5 micrograms/L chronic 

exposure (four day average) measured as a water column concentration) is used more frequently 

than the acute value.173 In the Grasslands waterways and Salt Slough, a more protective chronic 

value of 2 micrograms/L applies in consideration of sensitive listed species. The lentic 

conditions of water in the marshes were also a factor in setting these site-specific objectives.174 

The existing criteria for waterbodies listed in the table below, “Current Water Quality 
32

Standards,” refer to longer-term (chronic) and short-term (acute) exposure of aquatic life to 

selenium. The numbers represent water column concentrations of dissolved selenium and 

suspended particulates. All criteria listed below are set for aquatic life. The more stringent 

criteria in the Grasslands marshes and nearby areas are intended to protect threatened and 

endangered species.

Current Water Quality Standards

LOCATION CRITERIA REGULATORY ACTION

(Chronic) (Acute)

San Francisco Bay, 

including Suisun Bay and 

Marsh; Delta

5 microg/L – 

4 day average

20 microg/L – 

1 hr max 

National Toxics Rule – 1992

San Joaquin River from

Merced River to Vernalis

5 microg/L – 

4 day average

12 microg/L –

max 

instantaneous

Cent. Valley Region Basin Plan – 1996; 

National Toxics Rule – 1992 (chronic 

only)

Mud Slough;

San Joaquin River from 

Sack Dam to Merced River

5 microg/L – 

4 day average

20 microg/L –

max 

instantaneous

Cent. Valley Region Basin Plan – 1996; 

National Toxics Rule – 1992

Grasslands marshes; 

Los Banos State WMA; 

San Luis NWR; Salt Slough

2 microg/L –

monthly mean

20 microg/L –

max 

instantaneous

Cent. Valley Region Basin Plan – 1996

The current selenium standards lack criteria specific to water-dependent wildlife,

175 do 

not account systematically for differences in the physical and chemical characteristics of 

waterbodies (e.g., lentic versus lotic water)176 and use a measure (water column concentration, 

determined through dose-response tests) that is not a consistent indicator of exposure and 

environmental risk, because it fails to account for variables such as food web characteristics177. 

Water column values developed in a dose-response methodology, for example, do not take into 

account the relative efficiency of food webs in concentrating selenium. An ‘efficient’ food web 

would be one involving a selenium-sensitive species with a diet including a seleniumconcentrating species (e.g., the clam, Corbula). Over the last decade EPA has been working 

with other agencies to expand the scientific knowledge of selenium and update regulatory tools.

Establishing a framework for regulating selenium that integrates protective requirements 

and implementation across a diverse watershed is challenging. For example, standards set to 

protect designated uses in lotic (flowing) systems may not protect downstream designated uses in 

a different environment in terms of hydrology, water chemistry, and food web relationships. 

Higher river flows can function to transport large, albeit dilute, loads of selenium that settle in 

quieter downstream locations susceptible to food web uptake. Recently presented data on 

concentrations of selenium in North Bay clams, which do not show a clear-cut decline in 

selenium despite reductions in water column concentrations in San Joaquin River water entering 

the Bay Delta Estuary, suggest that more information is needed to determine the relationship 

between river inputs and processes in the downstream environment that affect biotic uptake.

178

 

Several efforts are underway to revise and expand standards for selenium in the Bay 

Delta Estuary. At the national level, EPA plans to propose Clean Water Act Section 304(a) 

selenium guidance criteria for aquatic life for freshwater. The guidance criteria will include 
33

chronic values only, and will distinguish between flowing and standing waters. These guidance 

criteria will form the basis for adopting protective water quality standards expressed as tissue 

concentration of selenium in fish egg or ovary and a corresponding water column concentration, 

where tissue concentration data are not available. Concentrations in tissue, such as bird eggs or 

fish tissue, better indicate actual exposure and, in combination with food web information, 

provide a basis for deriving site-specific numeric water column values. 

The revised national guidance criteria will be supplemented by regional efforts. EPA 

Region 9, in conjunction with the USGS, USFWS, and NMFS, and pursuant to its obligations 

under the ESA, is developing criteria to protect threatened and endangered wildlife species, 

aquatic-dependent species and aquatic life in California. The first phase of this effort addresses 

the San Francisco Bay and Delta. It uses data on affected species and relies on the PresserLuoma ecosystem-based model, a model that accounts for food web processes and site-specific 

conditions. 179 This phase is scheduled for completion in 2011, followed by a second phase for 

statewide criteria (including the San Joaquin River and its tributaries).

ii. TMDLs and Implementation 

North San Francisco Bay, a three-mile reach of the San Joaquin River between Mud 

Slough and the Merced River confluence (downstream), and the six-mile reach of Mud Slough 

North downstream of the San Luis Drain are each listed as impaired for selenium.180 These 

Clean Water Act listings, which appear in the 2010 Integrated Report, are based principally on 

evidence of ambient selenium exceeding concentration-based standards.181 Reductions in 

selenium discharges from agriculture in the San Joaquin Basin have been a major factor in 

meeting water quality objectives in the San Joaquin River between the Merced and Vernalis. 

Based on this evidence, the State Board recently declined to list this section of the River but 

retained the listing for selenium impairment in the reach with lower flow between Mud Slough 

and the Merced River.182 Delta waters are not considered impaired for selenium at the present 

time, largely on evidence of water column concentrations.

North Bay

Compliance with NPDES permit requirements by the oil refineries that discharge 

selenium in the North Bay has led to reduced loads and shifted the form of discharge towards 

selenate, rather than selenite.183 Estimates of selenium loadings prior to improvements required 

in 1998 are in the range of 1700-2900 kg/year; improved wastewater treatment post-1998 has 

reduced loadings to an estimated 200 to 550 kg/year.184 In March 2010, the San Francisco 

RWQCB amended four refinery permits, setting limits for total selenium, with a range from 34-

50 micrograms/L maximum daily, and 33-42 micrograms/L average monthly. The limits are 

based on a 10:1 dilution credit, with reference to the 5 microgram/L NTR criterion.185 The 

permit for a fifth refinery was amended in late 2009 to require similar limits. 

These point sources are also incorporated into a TMDL being developed for selenium in 

the North Bay. The San Francisco RWQCB began work on the TMDL in 2007 and is now 

coordinating the schedule and completion date with the forthcoming EPA wildlife criteria and 

aquatic life guidance criteria. While there are some nonpoint sources within the North Bay 
34

watersheds, the two major anthropogenic sources of North Bay selenium are the point source 

refineries and agricultural drainage from the San Joaquin Basin.

San Joaquin Grassland Bypass Project

The Grasslands Bypass Project, located west of the San Joaquin River and spanning the 

boundary between Merced County on the north and Fresno County to the south, is the current 

focus for implementation of selenium controls in the San Joaquin Basin. This 97,000-acre area 

is the northern portion of the much larger drainage problem area (730,000 acres total) described 

in the federal document, San Luis Unit Drainage Feature Reevaluation.186 The watershed 

affected by the Grasslands Bypass Project encompasses both irrigated agriculture and extensive 

private and publicly managed wetlands. Begun in 1995, the Project is significant because it 

includes most of the lands that discharge subsurface drainage to the San Joaquin River and Bay 

Delta Estuary.187 

The Grasslands Bypass Project is designed to achieve immediate protection of sensitive 

wetlands by routing agricultural drainage water away from this habitat into the federal San Luis 

Drain (a lined drainage canal) and from there into Mud Slough. Six miles downstream of this 

discharge point, Mud Slough enters the San Joaquin River at a reach with typically low flows. 

Over time, selenium load reductions implemented by the Grasslands drainers are intended to lead 

to fully meeting water quality objectives for all waters, including Mud Slough and the San 

Joaquin River. 

Three TMDLs, adopted between 1999 and 2002, are being implemented through the 

Grasslands Bypass Project.188 The regulatory framework laid out in the Basin Plan (and 

reinforced by conditions in a Waste Discharge Requirement) sets immediate compliance for the 

marshes and Salt Slough (2 ppb, monthly mean) and allows a longer period to meet existing 

standards for Mud Slough and the River (5 ppb, 4 day average).189 Some of the implementation 

framework is also provided in an Agreement for use of the Drain that has been negotiated 

between the U.S. Bureau of Reclamation (USBR) and the Delta-Mendota Water Authority.190

Implementation through drainage re-routing and reduction of selenium loads has resulted 

in meeting water quality objectives in the wetlands and Salt Slough and a 130 mile stretch of the 

San Joaquin River. Between 1996 and 2007, relying largely on control measures such as 

reduced water application, water conservation, and water recycling and use on salt tolerant crops, 

the project managers have reduced selenium loading to surface waters by approximately twothirds.191

 The Project has not, however, achieved the load reductions needed to fully meet the 

objectives by the compliance date of October 2010 set by the Central Valley RWQCB. During 

the 15-year project period, the project managers have tested various technologies beyond on-site 

drainage management to meet selenium load-reduction targets but recently reported to the 

Central Valley RWQCB that full success in meeting the October 2010 date was hampered by 

delays in expected state funding assistance and technical difficulties with treatment 

technologies.192 In a request to the State to extend the compliance period until 2019, the project 

managers expressed intent to introduce drainage treatment and disposal technologies that would 

result in eliminating discharges to the San Joaquin River, provided the funding and treatment 

technology issues are resolved. In approving this extension, the Water Boards emphasized that 
35

the Project is subject to a prohibition of discharge in 2019. Additionally, the project managers 

were directed to submit a progress report by January 2013 that includes a plan for compliance 

with the discharge prohibition and water quality objectives, even if drainage treatment is not 

found to be a feasible solution.193

Controlling selenium, once mobilized, is problematic. Feasible techniques for removal 

from the biotic system are not evident. Various approaches to removing selenium from water 

have been tested since Kesterson (e.g., use of algae or bacteria to remove selenium from water,

resulting in bioavailable forms that can pose a disposal problem). Currently, membrane 

technologies (reverse osmosis) are also being investigated.

The amount of selenium stored in the San Joaquin Basin is such that contamination in the 

Basin and Delta can be expected for years - possibly centuries.194 Unlike contaminants that can 

be readily reduced by ending use, selenium is now so widely distributed through the groundwater 

of the west side of the San Joaquin Basin that it can continue to be a problem even with efficient 

agricultural irrigation and drainage activities. The situation suggests a need for sustained 

management and regulatory strategies, as well as a continued commitment to research and 

assessment.195

c. Request for Public Comment 

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information and citations that support your comments.

1. What, if any, additional information is available to better characterize selenium sources, 

loadings and impacts within the watershed of the Bay Delta Estuary? 

2. What data, studies, and analytical techniques (for example, models) could be used to 

improve our understanding of the physical processes, including surface-groundwater 

interactions, controlling selenium mobilization and transport to and within the Bay Delta 

Estuary?

3. What data are needed to track selenium impacts in the Bay Delta ecosystem as currently 

configured, and to evaluate potential impacts of selenium under changed flow and transport 

conditions into and within the Delta? 
36

4. Pesticides

a. Aquatic Resource Issues

General Information

Pesticides are any substance or mixture of substances intended for preventing, destroying, 

repelling, or mitigating pests. They include products such as insecticides, herbicides, fungicides, 

rodenticides, piscicides, and antimicrobials. Pesticides are applied indoors and outdoors to 

structures and landscapes, in urban, suburban and agricultural areas. They are used to control 

disease-causing or other harmful organisms, including rodents, insects, and weeds that threaten 

crops and property. Pesticides can, however, present a risk to human health and the environment 

because they are designed to adversely affect living organisms.196

Pesticides can cause water quality problems when they are deposited into aquatic 

environments where they are potentially toxic to non-target organisms. Pesticides may be 

transported to aquatic sites long distances from application areas by precipitation and overland 

flow, irrigation runoff and return flow, POTW and stormwater discharges, and atmospheric drift. 

The USGS National Water Quality Assessment Program analyzes surface waters throughout the 

United States for pesticides and found that 100% of streams examined contained at least one 

pesticide; more than 56% of surface water samples contained one or more pesticides in 

concentrations exceeding aquatic-life benchmarks.197

Pesticides in the Bay Delta Estuary

More than twenty years of water quality monitoring show pesticides present in 

California’s Central Valley waterways, including the Bay Delta Estuary, at concentrations that 

affect aquatic ecosystems.198 The Central Valley RWQCB measured insecticides in irrigation 

return flows and receiving waters and established a connection between elevated pesticide levels 

and toxicity events in the Sacramento and San Joaquin Rivers and the Bay Delta Estuary 

beginning in the late 1980’s. This work documented many toxicity events related to pesticide 

loadings including: (1) toxicity to striped bass (Morone saxatilis) larvae, local invertebrate 

(Neomysis mercedis) and standard test invertebrate (Cerodaphnia dubia) in the Sacramento 

River during 1987-1990 from rice irrigation return flows;199 (2) invertebrate toxicity along a 43-

mile stretch of the San Joaquin River about 50% of the time between 1988 and 1990;200 (3) 3-day 

and 12-day invertebrate toxicity events at two sampling locations within the Bay Delta Estuary in 

1993 related to orchard insecticides;201 (4) consistent invertebrate toxicity in the mid-1990’s 

from insecticides in urban stormwater runoff that discharges directly to the Bay Delta Estuary 

from Central Valley and Bay Area Cities;202and (5) multiple diazinon toxicity events in the San 

Joaquin River at Vernalis, Sacramento Slough, and Orestimba Creek during January and 

February of 1996 and 1997.203 Algal toxicity was also observed as a result of herbicides in 

combination with elevated copper and zinc.204 More recent research documents toxic conditions 

for invertebrates caused by pyrethroid pesticides on a 30 km stretch of the American River, a 

4. Are there additional selenium control methods or programs that should be considered for 

reducing selenium inputs and impacts? 
37

tributary to the Sacramento River and Bay Delta Estuary, in the winter of 2009 from urban 

stormwater discharges.205 The majority of this toxicity was attributed to bifenthrin.

Aquatic habitat designated uses are impaired in all of the Bay Delta Estuary waterways 

by various pesticide pollutants including: Group A pesticides (aldrin, endrin, heptachlor, 

heptachlor epoxide, hexachlorecyclohexane (including lindane), endosulfan, and toxaphene), 

chlordane, dieldrin, chlorpyrifos, diazinon, DDT, and unknown toxicity.206 Tributaries upstream 

of the Bay Delta Estuary are also impaired for many different current-use pesticides including, 

but not limited to, bifenthrin, dimethoate, dacthal, malathion, diuron, simazine, trifuluralin, and 

cis-permethrin.207 In addition, pesticide investigations in the Bay Delta Estuary and upstream 

tributaries indicate that the source contaminant for “unknown toxicity”208 most likely involves 

current-use pesticides, which have been detected in surface waters throughout the Bay Delta 

Estuary (e.g., diazinon and bifenthrin).209

Sources of pesticides to the Bay Delta Estuary include urban point source (POTW and 

stormwater outfalls) and agricultural nonpoint source discharges. Analysis by the Urban 

Pesticide Pollution Prevention project of data from the California Department of Pesticide 

Regulation (DPR) indicate that approximately half of all California pesticide use, as measured by

weight of active ingredients, occurs in urban areas.210 Examples of urban pesticide use include 

indoor pest control and flea and tick shampoos and outdoor landscape and pest control 

application. In the greater Bay Delta Estuary watershed211 approximately 8,430 tons (active 

ingredient) of 160 different pesticides212 were applied in 2006 to control various agricultural and 

urban pest problems.213 Some groups of pesticides are associated with urban usage while others 

are primarily agricultural. Urban stormwater, runoff, and POTWs are the primary source of 

pyrethroid pesticides, while agriculture remains the primary source of organophosphate (with the 

exception of malathion) pesticides.214 

Pesticides and the Bay Delta Estuary Ecosystem Collapse

The relationship between pesticide toxicity and the long-term decline and recent plunge 

in pelagic fish populations is not clear.215 One evaluation reported that maximum concentrations 

of measured pesticides were two to four orders of magnitude below established 96-hour LC50s 

(lethal concentration at which 50% of test organisms die) for many fish.216 However, numeric 

water quality criteria protective of aquatic life are usually lower than the 96-hour LC50; for 

example, the Central Valley RWQCB considers one tenth of a well established 96-hour LC50 for 

the most sensitive aquatic species as the daily maximum exposure to an individual pesticide 

when numeric criteria and other toxicological data are not available. 217 In addition, exposure to 

multiple pesticides for time frames that exceed 96 hours, coupled with other physical stressors, 

may have lethal or sublethal impacts that cause or contribute to toxicity at lower concentrations 

than estimated 96-hour LC50, EC50s (concentration that has a specific survival effect such as 

impaired swimming for 50% of the test population), or lowest observed effect concentration. 

Larval and juvenile stages of some important pelagic species, including delta smelt, occurs in the 

late winter and spring overlapping with the storm season and peak concentrations of pesticides in 

the Bay Delta Estuary.218 These exposures could result in direct acute and/or chronic toxicity to 

pelagic fish or an indirect effect to fish populations from toxicity to prey items. 
38

Cellular and tissue abnormalities found in delta smelt and striped bass have been linked 

with insecticide exposure and reduced growth. A 3-year exposure study of delta smelt to 

pesticides in the Bay Delta Estuary spanning the years 1998 to 2000 shows that peak densities of 

larval and juvenile delta smelt overlap with elevated concentrations of pesticides, and that delta 

smelt are exposed to complex pesticide mixtures for a minimum of 2-3 weeks.219 Approximately 

10% of delta smelt in this experiment had fragmented DNA in blood cells, an established effect 

of pyrethroid pesticides and other stressors.220 Mixtures of pesticides measured in this study 

contained between 2 and 14 different pesticides at each sampling site. Striped bass researchers 

observed pesticides and other contaminants in striped bass eggs; brain, abdominal, and fin 

lesions in more than 65% of tested juveniles; and abnormal brain, liver, and overall development 

in river collected striped bass.221 

Pesticide toxicity to prey may contribute to the long-term decline and recent drop in 

pelagic fish populations by limiting food availability or by contributing to fish toxicity through 

consumption. Some aquatic invertebrates are more vulnerable to pesticide toxicity222 and make 

up a considerable portion of the diet for larval and juvenile pelagic fish.223 Invertebrate prey 

items could experience toxicity during periods of peak pesticide discharges to the Bay Delta 

Estuary, limiting available food for larval and juvenile pelagic fish. This is consistent with 

observed decline in zooplankton densities in the freshwater portion of the Bay Delta Estuary.224 

Other stressors such as declining phytoplankton primary production and excessive nutrient 

loading could contribute to the zooplankton decline as well.

The two pesticide groups of recent concern and attention are organophosphates (e.g., 

diazinon and chlorpyrifos) and pyrethroids.225 Both are insecticides, designed to kill 

invertebrates. Aquatic habitat designated uses are impaired in the Bay Delta Estuary due to the 

presence of organophosphate (OP) pesticides diazinon and chlorpyrifos.226 Use of OP 

pesticides has been replaced in the urban market with pyrethroid pesticides.227 Pyrethroids are 

very toxic to fish and invertebrates with 96-hour LC50s generally lower than 1 part per billion 

and “effect concentrations” (e.g., impaired swimming) approaching detection levels in the range 

of low to medium part per trillion.228 There are many other pesticides of concern, including, for 

example, herbicides and carbamates, but they have not received the recent attention focused on 

pyrethroids and organophosphates.229

Interaction between Multiple Stressors

The diversity and high volume of pesticides applied in the San Francisco Bay watershed 

that eventually emerge in the Bay Delta Estuary raise the possibility of interactive toxicity from 

complex pesticide mixtures and/or pesticides interacting with other chemical, physical, or 

biological stressors. Interactions of greatest concern are additive and greater than additive 

responses. Additive responses increase toxic conditions by an amount that is approximately 

equal to the summation of the toxicity elicited from individual stressors. Greater than additive 

responses increase toxic conditions by an amount greater than the summation of the toxicity 

elicited from individual stressors. Additive and greater than additive relationships result in toxic 

responses in aquatic organisms at lower contaminant concentrations than produced by exposure 

to individual contaminants.
39

Many studies identify interactive effects between pesticides and a resulting increase in 

toxicity to aquatic organisms. Additive toxicity to organisms produced by exposure to binary 

combinations of OP insecticides,230 herbicides,231 and carbamate/OP pesticides232 has been 

demonstrated in species and pesticides that commonly occur in the Bay Delta Estuary and its 

tributaries. Greater than additive toxicity to aquatic organisms has also been demonstrated with 

OP and pyrethroid combinations233 and OP and herbicide (atrazine and cyanizine) combinations 

that commonly occur in the Bay Delta Estuary.234 

Data Gaps

Data gaps are substantial regarding pesticide use, sources, toxicity, and contribution to 

the Bay Delta Estuary ecosystem collapse. It is difficult to accurately estimate source 

contributions of land-based pesticide applications due to an incomplete record of pesticide use, 

inadequate water quality monitoring data and the diversity of current-use pesticides.235 DPR

collects information on pesticide use that is more detailed than required by most other states; 

nonetheless, an estimated 70% of pesticide use does not require reporting (e.g., home and garden 

use).236 Information documenting the concentration of pesticides in waterways does not exist for 

many pesticides. One evaluation reported that less than half of the 160 different pesticides 

documented in the Bay Delta Estuary watershed are analyzed in water quality monitoring 

programs.

237

 

Established toxicity testing using individual contaminants over four days with test 

organisms may not fully represent toxicity to organisms in receiving waters. Unlike organisms 

in laboratory toxicity testing procedures, aquatic organisms in the Bay Delta Estuary are exposed 

to multiple stressors including chemical (contaminants), physical (water exports, salinity, 

temperature, turbidity) and biological (invasive species) stressors. The Central Valley RWQCB 

reports that approximately 100 different pesticides have been measured in rural and urban water 

bodies throughout the Central Valley.238 Potential interactive effects between contaminants 

and/or physical and biological stressors are not identified by establishing toxicity endpoints for 

individual pesticides in ideal laboratory conditions. In addition, observations within the Bay 

Delta Estuary and Central Valley tributaries illustrate that contaminant exposure times are at 

least four days and often much longer than the conventional 96-hour toxicity testing.239 Some of 

these issues are addressed by research and toxicity monitoring in receiving waters and 

procedures for identifying pollutants responsible for toxic response. 

Finally, the relative contribution of pesticide contamination to the recent collapse in 

pelagic fish populations and other ecosystem changes in the Bay Delta Estuary, such as the 

decline in zoo- and phytoplankton, is not straightforward. Research summarized above indicates 

that pesticide concentrations in the Bay Delta Estuary are below estimated acute toxicity 

thresholds for pelagic fish, but data indicating pesticides are responsible for fish abnormalities 

may be evidence of chronic toxicity causing population-level impacts to pelagic fish. There is 

evidence that ambient pesticide concentrations are acutely toxic to invertebrate prey items for 

pelagic fish; however, it unclear whether pelagic fish populations have declined due to food 

limitation. Lastly, conventional toxicity testing generally does not capture the negative impact 

on the aquatic ecosystem from multiple stressors present in the Bay Delta Estuary.240
40

b. Regulation under FIFRA

Pesticide regulation under FIFRA affecting Bay Delta Estuary aquatic resources is 

presently dominated by ongoing litigation involving the ESA. 

In the first ESA case, Washington Toxics Coalition v. EPA,

241 the plaintiffs alleged that 

EPA needed to consult with the NMFS over the potential effects on West Coast salmonids of 

registering 55 pesticides. This case covered salmonid watersheds in Washington, Oregon, and 

California, and included the Bay Delta Estuary and its tributary watersheds. Pursuant to a 

consent decree issued in 2004, EPA conducted a review of the possible effects of pesticides on 

these salmonids. After determining that there may be effects on 37 of the salmonid species, EPA 

initiated consultations with NMFS under Section 7 of the ESA. 

Given the number of species and pesticides involved, EPA and NMFS have been 

conducting the consultations in stages, grouping the pesticides into manageable sets. The first 

NMFS biological opinion under this process, which considered the widely used pesticides 

chlorpyrifos, diazinon, and malathion, was issued on November 18, 2008.242 EPA responded to 

the NMFS biological opinion in its letter of September 10, 2009, outlining its proposals for 

restricting the use of these pesticides under FIFRA in the Bay Delta Estuary region. More 

recently, on May 14, 2010, EPA committed to implement revised pesticide labeling requirements 

for these pesticides, creating additional specific pesticide application limitations (buffers, 

concentrations) designed to prevent the introduction of these pesticides to waterways used by 

listed salmonids.243

Under the consent decree, this process of consultation will continue for each of the 37 

pesticides determined by EPA to have potential adverse effects on listed salmonids. During the 

pendency of these consultations, application of the named pesticides is governed by a court order 

prescribing applications methods and watercourse setbacks.244

A second case involving pesticides in the Bay Delta Estuary is Center for Biological 

Diversity v. EPA,

245 (CBD v. EPA). In this case, the plaintiffs alleged the need for EPA to 

consult under the ESA with the USFWS over the possible adverse effects on 11 listed terrestrial 

and aquatic species in the greater San Francisco Bay Delta area of 75 registered pesticides. 

These species include the delta smelt and the tidewater goby, species that inhabit the Bay Delta 

Estuary. The two cases involve many of the same pesticides.

On May 17, 2010, the U.S. District Court issued a stipulated injunction in CBD v. EPA. 

Although there are some differences, the stipulated injunction roughly followed the model of 

Washington Toxics Coalition. EPA agreed to conduct initial assessments of the ingredients in 

each of the 75 pesticides and, where potential effects to species are identified, consultation with 

the USFWS would be carried out. Again, given the long list of pesticides and listed species 

involved, the stipulated injunction breaks this process into manageable groups for evaluation. 

EPA is not asking for public comment on the pesticides FIFRA litigation in this ANPR. 

Those two cases are active and under judicial supervision. As a part of that litigation, the public 

has had several opportunities to comment on the nature of the stipulated injunctions and the draft 
41

biological opinions being developed pursuant to the litigation. This information is included here 

to explain how EPA is addressing pesticides in the Bay Delta Estuary under one of the two major 

federal statutes regulating pesticides. Taken together, the evaluations and consultations being 

prepared under the FIFRA litigation cover both the major ESA-listed pelagic fish and the ESAlisted salmonids in the Bay Delta Estuary system.

c. Regulation under the Clean Water Act

Pesticides fall within the scope of the Clean Water Act in addition to regulation under 

FIFRA. The primary areas of current interest in the Clean Water Act regulation of pesticides in

the Bay Delta Estuary are: (1) developing chemical specific (numeric) water quality criteria; (2) 

developing TMDLs for waters impaired by pesticides; (3) addressing agricultural pesticides; (4) 

addressing pesticides in stormwater discharges through permits; and (5) issuing a general 

NPDES permit for the discharge of pesticides into waters of the U.S. 

i. Water Quality Standards 

Water quality standards are the foundation for regulating pesticides in California under 

the Clean Water Act. Water quality standards, composed of water quality criteria and designated 

uses, for the Bay Delta Estuary are contained in three basin plans: San Francisco Bay Basin Plan 

(SF Bay Basin Plan), San Francisco/Sacramento-San Joaquin Delta Estuary Basin Plan (Bay 

Delta Estuary Basin Plan) and the Water Quality Control Plan for the Sacramento and San 

Joaquin River Basins (Sacramento/San Joaquin Basin Plan). The Sacramento/San Joaquin Basin 

Plan contains narrative water quality criteria for pesticides as a group of pollutants, numeric 

criteria for a few individual pesticides, and narrative toxicity criteria that are relevant when 

pesticides are the source of aquatic toxicity.246 The SF Bay Basin Plan contains a narrative 

toxicity criteria, similar to the Sacramento/San Joaquin Basin Plan, but does not contain narrative 

or numeric criteria for pesticides as a group or for individual pesticides.247 The Bay Delta 

Estuary Basin Plan does not contain water quality criteria that directly regulate pesticide 

concentrations.248

The State Board recently proposed statewide numeric toxicity criteria in its Policy for 

Toxicity Assessment and Control.

249

 The proposed numeric toxicity criteria are expressed as 

statistical endpoints which represent the toxicant response that causes a given percent reduction 

in a biological measurement. The proposed chronic toxicity criterion establishes an unacceptable 

level of chronic toxicity consistent with the in-stream toxicant concentration at which 25% or 

more of the test organisms show adverse biological effects. The proposed acute criterion 

establishes an unacceptable level of acute toxicity consistent with the in-stream lethal toxicant 

concentration that affects 20% or more of the test organisms. 250

There are seven elements in the narrative toxicity water quality criteria contained in the 

Sacramento/San Joaquin River Basin Plan. Four of these elements are most relevant to this 

ANPR and state: (1) no individual pesticide or combination of pesticides shall be present in 

concentrations that adversely affect designated uses; (2) discharges shall not result in pesticide 

concentrations in bottom sediments or aquatic life that adversely affect designated uses; (3) 

pesticide concentrations shall not exceed those allowable by applicable antidegradation policies; 
42

and (4) pesticide concentrations shall not exceed the lowest levels technically and economically 

achievable. When numeric criteria are not adopted for individual pesticides and other 

information such as lowest observed effect and no observed effect concentrations for individual 

pesticides are not available, the Central Valley RWQC uses a figure of one tenth of the 96-hour 

LC50 for the most sensitive species tested as the upper limit or daily maximum for the protection 

of aquatic life.251

There are two numeric criteria for individual pesticides: diazinon (0.016 micrograms/L 1-

day average; 0.010 micrograms/L 4-day average) and chlorpyrifos (0.025 micrograms/L 1-day 

average; 0.015 micrograms/L 4-day average).252 The narrative toxicity criteria in the 

Sacramento/San Joaquin River and the SF Bay Basin Plans (under “Population and Community 

Ecology”) generally prohibit concentrations of toxic substances that cause acute or chronic 

toxicity to aquatic life.253

The Central Valley RWQCB is developing the Pesticides Basin Plan Amendment 

(Pesticides BPA) to address pesticide water quality impairments including interactive effects. 

Some objectives of the Pesticides BPA include identifying: (1) streams that should fully support 

aquatic life in the absence of elevated contaminant levels; (2) pesticides that present the greatest 

risk to aquatic life; (3) numeric metrics, including water quality criteria, that will protect aquatic 

life from the interactive or individual effects of high-risk pesticides; and (4) best management 

practices to prevent pesticide impacts.254

The Pesticides BPA is divided into two phases, with additional work on supporting 

studies. Completed supporting studies identify twenty eight individual pesticides as having a 

high overall relative risk to aquatic life, ten individual pesticides with moderate risk,255 and draft 

numeric water quality criteria for six of the high relative risk pesticides: cyfluthrin, lambda 

cyhalothrin, bifenthrin, malathion, diazinon, and diuron.256 Phase I of the BPA, focused on OP 

pesticides diazinon and chlorpyrifos, will include proposed water quality criteria and TMDLs for 

diazinon and chlorpyrifos-impaired waterbodies. A draft staff report for Phase I is anticipated in 

late 2010. Phase II will focus on developing numeric water quality criteria and TMDL 

development for pyrethroid and other high-risk pesticides, and is scheduled to be completed in 

late 2012.257

ii. TMDLs

The Central Valley RWQCB adopts TMDLs to address water quality impairments. The 

2010 303(d) list recently adopted by the State Board identifies violations of state water quality 

standards as a result of pesticide concentrations exceeding narrative and numeric criteria causing 

impairments to aquatic habitat designated uses in all Bay Delta Estuary Waterways.258 The 

Central Valley RWQCB adopted TMDLs and TMDL implementation plans addressing 

organophosphate pesticides in the Bay Delta Estuary and upstream watersheds and is developing 

an organochlorine TMDL for the Central Valley. These TMDLs are designed to reduce 

pesticide concentrations in the Bay Delta Estuary and its upstream tributaries with the goal of 

attaining water quality standards.

The draft organochlorine pesticides TMDL addresses legacy pesticides whose 
43

registrations were cancelled by EPA in the 1970’s. This persistent class of contaminants is still 

detected in water, sediment, and biological tissue at levels high enough to warrant listing Bay 

Delta Estuary and Central Valley tributaries on the 2010 303(d) list. Organochlorine pesticides

include (but are not limited to) dichlorodiphenyltrichloroethane (DDT), aldrin, endrin, 

heptachlor, hexachlorecyclohexane, and endosulfan (still in use but being phased out). The 

proposed TMDL includes numeric targets for the water column, sediment, and fish tissue derived 

from the existing narrative criteria.259

The Central Valley RWQCB has adopted TMDLs and TMDL implementation plans for 

diazinon and chlorpyrifos in the Sacramento and Feather Rivers, Sacramento County urban 

creeks, San Joaquin River, and the Sacramento-San Joaquin Delta (Bay Delta Estuary) 

waterways. The diazinon and chlorpyrifos TMDLs for these waterways include wasteload 

allocations for point sources and load allocations for non-point sources that address the additive 

toxicity of diazinon and chlorpyrifos. Point sources are addressed by implementing effluent 

limitations in NPDES permits. Agricultural pesticide sources are partially addressed through the 

Central Valley RWQCB Irrigated Lands Regulatory Program (ILRP).

260

iii. Regulation of Agricultural Discharge

The ILRP is part of a unique regulatory framework in California that addresses pesticide 

water pollution. Historically, the Central Valley RWQCB addressed agricultural pesticide 

discharges into the Central Valley and Bay Delta Estuary waters through Conditional Waivers 

issued under the California Water Code. In 2003, in response to reform legislation adopted by 

the State Legislature, the Central Valley RWQCB adopted a Conditional Waiver of Waste 

Discharge Requirements for Irrigated Lands (renewed in 2006) and directed staff to develop 

environmental documentation for a long-term Irrigated Lands Regulatory Program.261

The Coalition Group Conditional Waiver of Waste Discharge Requirements for 

Discharges from Irrigated Lands is a general permit that waives the requirement for an individual 

permit for entities that join a “coalition group.” Coalition groups conduct water quality 

monitoring to determine the effect of member discharges on water quality. If specific water 

quality problems are identified in the monitoring reports, coalition groups create management 

plans and coordinate with members to implement best management practices that reduce 

pesticides or other contaminant loadings to waters.262 The current Irrigated Lands waste 

discharge requirement waiver for irrigated lands in the Central Valley will expire in June 2011. 

It may be renewed or the Central Valley RWQCB may transition to implementation through the 

proposed long-term ILRP.

The Central Valley RWQCB released a draft programmatic Environmental Impact Report 

(PEIR) for the proposed long-term ILRP in July 2010 for public comment. The overall goals of 

the long-term ILRP are to (1) restore and/or maintain the highest reasonable quality of state 

waters considering all the demands being placed on the water; (2) minimize waste discharge 

from irrigated agricultural lands that could degrade the quality of state waters; (3) maintain the 

economic viability of agriculture in California’s Central Valley; and (4) ensure that irrigated 

agricultural discharges do not impair access by Central Valley communities and residents to safe 

and reliable drinking water.263 The Final EIR and Central Valley RWQCB action are planned for 
44

2011.264

iv. Stormwater Permits 

Stormwater discharges from MS4s, associated with construction activity, and associated 

with industrial activity have been shown to carry pesticides to surface waters and affect water 

quality.265 The current NPDES permits for these stormwater discharges, to some degree, address 

the issue of pesticides in stormwater discharges, in addition to other pollutants. 

In California, stormwater discharge permits are issued by the Water Boards under the 

authority of the Clean Water Act. There are six individual MS4 stormwater permits potentially 

affecting the Bay Delta Estuary, as well as a statewide general permit for smaller dischargers.266 

Much of the area surrounding the Bay Delta Estuary is covered by one of these stormwater 

permits.

The MS4 permit for Sacramento County and associated cities requires permittees to 

implement a Pesticide Plan approved by the Central Valley RWQCB. The plan addresses the 

permittees’ use of pesticides including diazinon, chlorpyrifos, and other lower priority pesticides. 

The permit requires implementation of Integrated Pest Management practices, public education 

and outreach, and studies of local or regional sales and use of residential and commercial pest 

control products potentially found in stormwater runoff.

The California Construction General Permit (CA CGP)

267 was issued by the State Board 

on September 2, 2009 and expires in 2014. The CA CGP requires that stormwater discharges 

not contain pollutants that cause or contribute to an exceedance of any applicable water quality 

objective. The CA CGP requires that all dischargers develop a sampling and analysis strategy 

for monitoring pollutants that are not visually detectable in stormwater. Of significant concern 

for stormwater discharges associated with construction activity are the pollutants found in 

materials used in large quantities at construction sites throughout California and exposed 

throughout the rainy season, in particular glyphosate (herbicide), diazinon and chlorpyrifos 

(pesticides), nutrients (fertilizers), and molybdenum (lubricants). Diazinon and chlorpyrifos are

commonly used by landscape professionals and may trigger sampling and analysis requirements 

if these materials come into contact with stormwater. 

On December 1, 2009, EPA promulgated the final Construction and Development 

Effluent Limitations Guideline and Standards (C&D ELG) which state that construction site 

operators must “[d]esign, install, implement, and maintain effective pollution prevention 

measures to minimize the discharge of pollutants. At a minimum, such measures must be 

designed, installed, implemented and maintained to...[m]inimize the exposure of building 

materials, building products, construction wastes, trash, landscape materials, fertilizers, 

pesticides, herbicides, detergents, sanitary waste and other materials present on the site to 

precipitation and to stormwater.”268 Any new or reissued NPDES permit for stormwater 

discharges associated with construction activity in California must incorporate the applicable 

requirements in the C&D ELG.269

The California Industrial Stormwater General Permit270 (CA IGP) was issued by the State 
45

Board in 1997. The State Board noticed a draft reissuance of the Industrial Stormwater General 

Permit in 2005; however no final action has been taken on the reissuance. The current permit 

requires that operators reduce or prevent pollutants in stormwater discharges associated with 

industrial activity and ensure that such discharges will not cause or contribute to an exceedance 

of any applicable water quality standards. Additionally, the CA IGP addresses stormwater and 

non-stormwater coming into contact with “significant materials” on industrial sites, defined in 

the permit to include pesticides. 

The stormwater permit programs described above may not cover all stormwater 

discharges of concern. If EPA or California finds that other currently unregulated stormwater 

discharges are contributing pollutants to waters of the U.S. or contributing to water quality 

standards exceedances, EPA and/or California may require those discharges to obtain NPDES 

permits through “residual designation.”271 Examples of currently unregulated point source 

discharges of stormwater include small MS4s currently outside urbanized areas that may not 

meet the population threshold for a regulated small MS4 and stormwater discharges from 

impervious surfaces, such as commercial facilities, retail centers, or residential subdivisions. 

As part of its implementation of the Phase I and II stormwater regulations, California has 

used its authority under 40 C.F.R. 122.35 to designate unregulated small MS4s as requiring 

NPDES permit coverage.272 EPA and/or California may designate additional discharges from 

unregulated MS4s to surface waters in the Bay Delta Estuary or its tributaries as necessary in 

order to address the impacts of pesticides on the water quality.

Alternatively, instead of designating discharges from MS4s, EPA and/or California may 

designate individual or categories of stormwater discharges for regulation under the Clean Water 

Act. For example, EPA Region 1 (New England) is in the process of using the residual 

designation authority under 40 C.F.R. 122.26(a)(9)(i), to designate and require an NPDES permit 

for stormwater discharges from two or more acres of impervious surface in the Charles River 

watershed in Massachusetts. While the Charles River residual designation and proposed NPDES 

permit are not focused exclusively on the discharges of pesticides, a byproduct of regulating 

stormwater discharges from developed sites will be a reduction in various pollutants, including 

pesticides, discharged to surface waters. The Region 1 proposed permit includes a provision for 

the proper management of landscaped areas in the watershed that includes the requirement to 

“minimize the risk that any landscaped pervious surfaces will contribute pollutants to stormwater

discharges from the [site]...[a]t a minimum, this shall include assuring the proper storage, use, 

and disposal of fertilizers, pesticides, and herbicides....”273 To date, the residual designation 

approach has not been proposed or used in the Bay Delta Estuary.

Another approach to addressing stormwater discharges is being undertaken by EPA 

Region 3 and the EPA Office of Water in the Chesapeake Bay watershed.274 In a nationwide 

effort to revise EPA’s stormwater regulations,275 EPA may propose revisions to the existing MS4 

regulations for stormwater discharges from MS4s under Clean Water Act Sections 402(p)(3)-(4) 

and (p)(6) and/or the designation and regulation of stormwater discharges from developed sites 

under Clean Water Act Section 402(p)(6). As part of any national rule, EPA is considering 

designating stormwater discharges from newly developed and redeveloped sites to protect water 

quality; revising the scope of regulated MS4 discharges subject to NPDES permitting; addressing 
46

discharges from existing development (e.g. to address existing impairments in receiving waters). 

EPA is considering Chesapeake Bay-specific provisions, such as expanding the regulatory 

coverage to a greater number of discharges than required under any national stormwater rule. 

This includes the consideration of Chesapeake Bay-specific requirements that may be needed to 

meet the TMDL wasteload allocations. While this Region 3 and EPA Office of Water effort is 

not focused exclusively on the discharges of pesticides, regulating stormwater discharges from 

developed and redeveloped sites and revising the requirements in MS4 permits will likely reduce 

multiple pollutants, including pesticides.

v. General NPDES Permits for Aquatic Pesticide Application 

On March 12, 2001, the Ninth Circuit Court of Appeals, in Headwaters, Inc. v. Talent 

Irrigation District,

276 held that discharges of pollutants from the use of aquatic pesticides to 

waters of the United States require coverage under a Clean Water Act NPDES permit. As a 

result, in 2004, the State Board issued general permits for the discharge of aquatic pesticides to 

surface waters for vector control277 and weed control.278 Additionally, the State Board has 

released a preliminary draft general permit for adulticide to cover the discharge of residual 

pesticides to waters of the U.S. resulting from adult mosquito spray applications.279 Thus, in the 

Bay Delta Estuary, the application of pesticides directly to, over, or near, water may require 

permit coverage under either the State’s vector control general permit, the State’s weed control 

general permit, or the adulticide general permit that is currently being proposed by the State 

Board.

d. Request for Public Comment

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information with citations that support your comments.

1. What, if any, additional scientific information is available on (a) the effects of pesticides in 

stormwater discharges, or (b) the potential interactive effects of combinations of pesticides on 

aquatic resources in the Bay Delta Estuary?

2. What, if any, actions should EPA take under its authority to improve the effectiveness of 

regulating pesticide contamination of the Bay Delta Estuary watershed? 
47

3. How can the process for establishing numeric water quality criteria be streamlined while 

maintaining technical integrity? 

4. What are the benefits and constraints of using fish tissue in place of, or in addition to, water 

column concentrations when establishing water quality criteria for pesticides?

5. Are there testing protocols that would effectively and efficiently identify synergistic toxic

effects in the Bay Delta Estuary? 

6. What, if any, specific combinations of contaminants are of particular concern in the Bay 

Delta Estuary? 

7. Should EPA and our state partners move away from evaluating isolated aquatic species for 

one or two pollutants, and towards evaluations of water conditions more representative of the 

actual aquatic conditions in the Bay Delta Estuary? How might this be done? 

8. What new or revised effluent limitations, monitoring requirements or other permit 

requirements could be included in NPDES permits for discharges of pesticides from MS4s in the 

Bay Delta Estuary in order to better meet the regulatory standard of reducing discharges to the

maximum extent practicable? What information is necessary to determine permit requirements, 

such as identifying effluent limits that can effectively reduce ambient contaminant 

concentrations and restore designated uses? Please provide any available information on water 

quality benefits that may result from such requirements.

9. What new or revised effluent limitations, monitoring requirements or other permit 

requirements could be included in NPDES permits for stormwater discharges associated with 

construction activity and/or stormwater discharges associated with industrial activity to address 

pesticides? What information is necessary to determine permit requirements, such as identifying 

effluent limits that can effectively reduce ambient contaminant concentrations and restore 

designated uses? Please provide any available information on water quality benefits that may 

result from such requirements.

10. Should EPA use its residual designation authority at 40 C.F.R. 122.35 to designate currently 

unregulated small MS4s to ensure that municipalities have programs in place to control the 

discharge of pesticides in stormwater to the maximum extent practicable? What information is 

necessary to determine permit requirements, such as identifying effluent limits that can 

effectively reduce ambient contaminant concentrations and restore designated uses? Please 

provide any available information on water quality benefits that may result from such 

requirements.

11. Should EPA use its residual designation authority at 40 C.F.R. 122.26(a)(9)(i)(C)-(D) to 

designate currently unregulated stormwater discharges that contribute pesticides to surface 

waters? What information is necessary to determine permit requirements, such as identifying 

effluent limits that can effectively reduce ambient contaminant concentrations and restore 

designated uses? Please provide any available information on water quality benefits that may 

result from such requirements.
48

5. Contaminants of Emerging Concern

a. Aquatic Resource Issues

Nationally, researchers are documenting potentially significant effects on aquatic 

ecosystems from compounds that have not traditionally been considered or regulated. These 

“contaminants of emerging concern” (CECs) include pharmaceuticals, personal care products, 

solvent stabilizers, flame retardants, pesticides and other commonly used commercial and 

industrial compounds. These substances can be introduced into the aquatic environment through 

a variety of sources including municipal and industrial wastewater systems, urban stormwater, 

animal husbandry operations and agricultural runoff. 

Some of these substances may be endocrine disrupting chemicals (EDCs), which are 

exogenous substances that change endocrine function and cause adverse effects at the level of the 

organism, its offspring, and/or (sub)populations of organisms. EDCs can alter hormone levels, 

potentially resulting in the masculinization of female mollusks,280 the feminization of male fish, 

and reproductive effects.281 Of the CECs detected in surface waters of the U.S., EDCs have 

received the most attention because field studies have shown that very low concentrations of 

some of these compounds can significantly affect natural populations of aquatic vertebrates.

In San Francisco Bay (downstream of the Delta), the Bay Regional Monitoring Program 

began collecting data on CECs since 2001 and has generated a relatively extensive dataset for 

CECs in the Bay, with a few sampling locations in the Delta.282 Several pilot studies have 

collected data in the Delta and upstream tributaries but there are significant data gaps. Very few 

CECs are routinely monitored in the environment. Some Regional Water Boards have begun to 

include permit conditions for major POTWs to conduct special studies, technical reports and 

additional monitoring for CECs in their effluent.

Although there is not sufficient data in the published literature to adequately assess the 

ecological implications of CECs in the Bay Delta Estuary,283 there is ample evidence to warrant 

additional attention. Compounds that may be EDCs have been found in waters of the Central 

Valley and at particularly high levels in the Delta and Napa River.284 In addition, endocrine 

disrupting effects, such as skewed sex ratios in a population and developmental disruptions in 

individuals, have been found in fishes of the Delta.285 One researcher showed that sex ratios in 

adult striped bass were skewed toward males to the extent that the altered sex ratio might account 

for the near absence of young fish in recent years.286 Many more male than female silversides 

(Menidia beryllina) were found at an urban sampling site compared to an agricultural site in 

Suisun Marsh. This study also measured the effects of potential EDCs in the water from these 

sites on sensitive cell lines and found estrogenic activity at both sites, but significantly higher 

androgenic activity at the urban site.287 Evidence of low frequency endocrine disruption was 

found in 2005 in adult delta smelt collected in the Delta and Suisun Marsh. In this study, 9 of 

144 (6%) of adult delta smelt males were intersex, having immature oocytes in their testes.288

Like other contaminants, CECs exist in the environment in mixtures. Some studies (not 

in the Delta) have begun to look at interactive effects though much more research is needed to 

draw meaningful conclusions.
49

b. Regulatory Status 

On a national level, EPA’s strategy for addressing the effects of CECs includes 

improving science and public understanding; identifying partnership and stewardship 

opportunities; and taking regulatory action when appropriate.289 

There are currently no water quality aquatic life criteria or drinking water standards,

making data difficult to interpret.290 EPA is evaluating the potential impacts of CECs on aquatic 

life and developing an approach for determining protective levels for aquatic organisms. EPA 

uses guidelines established in 1985 to derive ambient water quality criteria (AWQC) for aquatic 

life.291 These guidelines consider acute effects (short-term effects such as survival) and chronic 

effects (longer-term effects such as reproduction) for traditional pollutants. Developing aquatic 

life criteria for CECs and potential EDCs may require modified methodologies along with effects 

endpoints not previously evaluated using the 1985 guidelines. For instance, potential EDCs may 

demonstrate low acute toxicity but cause reproductive effects at very low levels of chronic 

exposure. In addition, the effects of exposure on aquatic organisms during the early stages of life 

may not be observed until adulthood. Therefore, traditional toxicity test endpoints may not be 

sufficient for criteria derivation for these chemicals and the chemicals may also have specific 

modes of action that may affect only certain types of aquatic animals (e.g., vertebrates such as 

fish).

In response to this challenge, in June 2008, EPA developed a white paper detailing 

technical issues and recommendations to serve as a basis for modifying the 1985 guidelines to 

better address CECs and develop AWQC protective of aquatic life.292 This paper was reviewed 

by EPA’s Science Advisory Board.293 The SAB supports development of risk-based aquatic life 

criteria for EDCs which include consideration of probable direct and/or indirect impacts on food 

webs, ecological processes and services, and endangered or unique species of special value or 

concern. In addition, the SAB noted the potential for interactive effects that may occur in CEC 

mixtures in the environment and which may also interact with environmental variables such as 

temperature. 

EPA has developed new analytical test methods for particular CECs, although much such 

work remains to be done. Since the first reports that CECs were occurring in surface waters, 

questions have been raised regarding their presence in sewage influent, effluent and sludge. At 

the time of these first reports, no suitable analytical methods were available for these waste 

streams. EPA has developed two new analytical methods to identify and measure certain CECs, 

specifically, pharmaceuticals, steroids and hormones in sewage influent, effluent and sludge. 

These methods currently cover over 100 chemicals (74 pharmaceuticals and personal care 

products and 27 steroids-hormones) and three wastewater matrices (raw and treated sewage 

water and sludge). EPA has also revised the flame retardants (PBDE) analytical method. The 

contaminants in these methods are not currently regulated, nor have the methods been 

promulgated at 40 C.F.R. Part 136.294

In California, a workshop in 2009 brought together scientists, water quality managers, 

and stakeholders to initiate an effective CEC management strategy. Consensus was reached 

around certain findings and recommendations, including: (1) the current chemical-specific risk 
50

assessment approach is neither feasible nor cost-effective for prioritizing and managing the vast 

majority of CECs; (2) developing regulatory limits is premature given the state of knowledge; (3) 

flexible, multi-element prioritization framework is needed to identify compounds of highest 

concern; (4) a single master list of CECs that agencies could apply effectively across all 

applications is unlikely; (5) the interpretation of monitoring data and subsequent decisionmaking should be based on tiered, multiple thresholds; and (6) an adaptive management strategy 

is imperative to respond to rapidly changing knowledge.295

The “Policy for Water Quality Control for Recycled Water” adopted by the State Board 

in February 2009 included mandated monitoring of CECs in municipal recycled water.296 To 

provide guidance on implementing this aspect of the policy, the State Board tasked the Southern 

California Coastal Water Research Program (SCCWRP) with convening a Science Advisory 

Panel. The recommendations from that panel297 are under consideration by the State Board.298 

SCCWRP is convening another scientific panel to advise the State on how best to limit the 

impact of CECs on oceans, estuaries and wetlands.299

c. Voluntary Activities 

Federal, state and local agencies have experimented with voluntary source control efforts, 

such as “take-back” programs and events, which are collection methods aimed at reducing the 

quantity of unused pharmaceuticals entering the environment. Some communities have ongoing 

pharmaceutical take-back programs or community solid waste programs that allow the public to 

bring unused drugs to a central location for more appropriate disposal. In 2009, EPA partnered 

with the California Pharmacists Association, East Bay Municipal Utility District, California 

Association of Sanitation Agencies, TriTac, and others on the No Drugs Down the Drain 

campaign.

On October 12, 2010, President Obama signed the Secure and Responsible Drug Disposal 

Act of 2010. The bill establishes programs to safely dispose of unused or unwanted prescription 

drugs and controlled substances through community-based efforts, amends the Controlled 

Substance Act to allow the attorney general to develop drug disposal programs, and allows longterm care facilities to dispose of drugs on behalf of their residents.

In September 2010, EPA issued a draft guidance document, "Best Management Practices 

for Unused Pharmaceuticals at Health Care Facilities" for hospitals, medical clinics, doctors' 

offices, and long-term care facilities. It describes techniques for reducing or avoiding 

pharmaceutical waste, practices for identifying and managing unused pharmaceuticals, and 

applicable disposal regulations. EPA is revising the document based on public comment.

d. Request for Public Comment

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 
51

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information with citations that support your comments.

1. What, if any, additional information is available regarding the effects of CECs on aquatic 

resources in the Bay Delta Estuary?

2. What, if any, specific information exists to identify the sources and nature of discharges 

of CECs into the Bay Delta Estuary?

3. What, if any, monitoring mechanisms or methodologies are available to assist in 

identifying CECs?

4. What, if any, methods are most effective to minimize introduction of CECs into the Bay 

Delta Estuary?
52

Figure D. Low Salinity Zone (X2) in the Bay Delta Estuary

B. Protecting Estuarine Habitat, Fish Migration Corridors and Wetlands

1. Estuarine Habitat

a. Aquatic Resource Issues

For many species of fish and invertebrates in San Francisco Bay, ocean conditions and 

broad climatic changes drive population abundance, but estuarine species of Suisun Bay and the 

Delta are controlled by other factors.300 A number of factors are apparently important for the 

health of estuarine species, but the location of the low salinity zone (X2301) plays a large role, 

both historically302 and recently.

303

 The low salinity zone is the location of the greatest 

abundance of many pelagic organisms of the upper Bay Delta Estuary,

304 including the 

threatened delta smelt (Hypomesus transpacificus), the state-listed longfin smelt (Spirinchus 

thaleichthys) and juvenile striped bass (Morone saxatilis), the former premier sport fish of the 

Bay Delta Estuary. The average springtime location of the low salinity zone (X2) is also tied to 

the survival or abundance of a number of fish and larger invertebrates of the Bay Delta 

Estuary.305 The nature of the low salinity zone is also important for less desirable species. For 

one major invasive species, the overbite clam (Corbula amurensis) salinity variability is an 

important determinant of their distribution and impact.306 Given these correlations, X2 is an 
53

effective indicator of ecosystem conditions from year to year.307 The community-level, rather 

than species-specific, nature of X2 makes it uniquely suitable as a broad estuarine habitat 

protection standard.308 Climate change and associated sea-level rise are expected to make 

salinity distribution in the Bay Delta Estuary an even more important ecological driver than at 

present.309

Recent research suggests that the quantity and quality of low salinity estuarine habitat, as 

measured by the location of the 2 ppt salinity gradient or X2, has declined during the fall period 

since 1985.310 As shown in Figure E, the low salinity zone in the fall has moved upstream, 

especially after 2000. When the low salinity zone moves upstream, its areal extent shrinks as the 

low salinity zone is forced into the narrow, deeper channels of the interior Delta and away from 

the broad shallow shoals of Honker Bay and Suisun Bay downstream. Figure F reflects this 

correlation between the location of the low salinity zone and its areal extent. In the late 1990s, 

the median areal extent of this low salinity estuarine habitat was about 9000 hectares in the fall; 

since 2000, that habitat declined by about 78 percent. 

Figure E also shows the dramatic decline in the variability of the location (and therefore 

the extent) of low salinity habitat. Prior to 2000, the location of the low salinity zone during the 

fall varied significantly from year to year, based on springtime precipitation and releases from 

summertime carryover reservoir storage. The areal extent of low salinity habitat for smelt and 

striped bass in the fall thus also varied from year to year. 

Since 2000, the low salinity zone in the months of September through November (fall 

X2) has been consistently further upstream in the watershed in all water year types,311 in the 

western Delta (rather than fluctuating between the western delta and further west into Suisun 

Bay). This consistent upstream shift of the low salinity zone has greatly reduced areal extent of 

the fall habitats of delta smelt and young striped bass. This change in the fall X2 has also been 

associated both with increased upstream abundance of invasive clams312 and jellyfish313 and with 

declines in abundance of young striped bass and pre-spawning delta smelt.314 The combined 

indicators of adult delta smelt abundance and the location and extent of fall habitat appear to be a 

good predictor of subsequent summer delta smelt abundance.315
54

Figure E. Fall Location of Low Salinity Zone (X2) 1960-2010, by water year316

 (in kilometers)

Figure F. Habitat Size based on Fall Location of Low Salinity Zone (X2)

b. Regulatory Status

The State Board’s Water Quality Control Plan has included “estuarine habitat” as a 

designated use since 1989. Pursuant to the Clean Water Act, EPA reviews a state’s water quality 

standards to determine whether the state has adopted criteria that protect the designated water 

55

60

65

70

75

80

85

90

95

1960 1970 1980 1990 2000 2010

X2 

(distance in kilometers of 

low salinity zone from Golden Gate)

Year

Wet

Above Normal

Below Normal

Dry

Critical
55

uses.317 In the past, this review has included a consideration of physical, chemical, and 

biological parameters such as temperature and salinity.318 In 1995, the State Board adopted 

outflow requirements during the spring to protect the estuarine habitat designated use. These 

outflow requirements were based on the X2 concept and reflected several years of discussion and 

refinement in a collaborative effort between regulatory agencies and interested water export and 

environmental organizations. When adopted, the X2 standard was widely praised as a broad 

ecosystem standard that provided protection for estuarine species generally, as opposed to the 

individual species orientation of other regulatory measures.319 Although the degree of correlation 

between X2 and abundance has shifted somewhat for some species since 1994, analyses show 

that X2 remains an important factor affecting the suite of species that have declined since 

2000.320

The X2 standard, adopted by the State Board and approved by EPA in 1995 and restated 

in 2006, applies only in the spring months (February - June). During these months, most young 

salmonids are migrating downstream and most resident estuarine fishes are spawning. 

Correlations of X2 with species abundance or survival, upon which the standard was based, were 

highest for spring months. In many years springtime conditions in the Delta are driven by high 

precipitation and flood control activities rather than export operations. The 1995 Water Quality 

Control Plan was influenced by concerns raised during the 1987-92 drought, when springtime 

conditions were exceptionally more adverse than in preceding years. Most of the fish now listed 

under the ESA were listed in the years immediately following the 1987-92 drought. 

After adoption of the 1995 Water Quality Control Plan and the return of more normal 

springtime flows, most species of interest showed a resurgence in abundance. Delta smelt almost 

achieved the criteria for delisting identified in their ESA recovery plan,321 adult striped bass 

populations returned to levels not seen since the 1970s, threadfin shad were sharply rising in 

abundance and longfin smelt were achieving fairly high abundances.322 Around the year 2000, 

however, the well-sampled pelagic fishes all simultaneously declined.323 At the time of this 

decline, the location of the low salinity zone moved upstream during fall months of all years and 

was greatly reduced in areal extent. This change in habitat, and the proposed project operations 

to maintain these conditions into the future, was identified as a threat to the survival of delta 

smelt and as a degradation of its critical habitat.324 Consequently, the 2008 USFWS Biological 

Opinion on the impact of SWP and CVP operations on delta smelt included a provision to 

manage low salinity zone habitat in the fall.325 That provision mandates specific fall X2 values, 

and the associated areas of suitable habitat, during fall months after wet and above-normal water 

years.326 This fall X2 provision restores some of the fall habitat that characterized the Bay Delta 

Estuary until 2000.327 

The fall X2 requirement in the 2008 Delta Smelt Biological Opinion has been reviewed 

in two independent peer review processes.328 Both reviews supported the importance of habitat 

protection and the suitability of using X2 as a surrogate for that habitat. At the same time, both 

reviews also questioned the basis for the exact targets specified in the Opinion and supported the 

requirement for intensive study and monitoring of the effects of the requirement. The NAS 

review also questioned the predictive nature of the relationship for delta smelt abundance. 

Recent litigation over the ESA biological opinion on water export operations raised similar 

issues on the X2 approach.329
56

The State Board included the fall X2 flow prescriptions of the USFWS Biological 

Opinion for delta smelt in its recommendation for flows needed to broadly protect public trust 

resources, but did not recommend greater flows until the values of the Biological Opinion flows 

were analyzed and potential risks to cold water habitat for salmon spawning were avoided.330 

Likewise, the California Department of Fish and Game (DFG) recommended maintaining X2 

between 74 km and 81 km between September and November in wet and above normal years, 

but did not recommend greater flows unless studies show they will not compete with 

preservation of cold water pool resources needed for the protection of winter-run salmon.331

c. Request for Public Comment

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information with citations that support your comments.

1. What information is available on the effect of lower salinities in the western Delta on 

undesirable species such as Microcystis, overbite clams, or jellyfish? What, if any,

information is available to determine if an increase in low salinity habitat would affect the 

fate, concentration and distribution of nutrients and toxics that are potentially negatively 

affecting the estuarine food web?

2. Could the frequency, area, and/or duration of low salinity habitat be changed so as to 

achieve ecosystem benefits for the suite of species that use the low salinity zone? If so, how? 

Is historical data on inter- or intra- annual frequency of variability the best basis for setting 

goals or are there other bases that could be used? How might climate change impacts, 

including sea level rise, affect the size, frequency, and duration of low salinity habitat?

3. Are methods available for more systematically addressing ecological or biological 

connections between springtime X2 and subsequent fall X2 conditions? If so, what are they 

and what are their strengths and weaknesses?

4. Would changes in water system operations to move X2 seaward in the fall adversely affect

the reservoir storage needed to conserve salmonid fish spawning and other designated uses in 

the watershed? If so, under what conditions?
57

2. Fish Migration Corridors

a. Aquatic Resource Issues

San Joaquin Valley salmonid populations have suffered a long-term decline. Spring-run 

salmon that spawned on the upper San Joaquin were eliminated after the construction of the 

Central Valley Project’s Friant Dam in the 1940’s on the San Joaquin River near Fresno and the 

Mendota and Friant-Kern Canals. On average, over 90% of the San Joaquin River flow at Friant 

Dam has been diverted annually, resulting in dewatering of several reaches (totaling 60 miles) of 

the main stem San Joaquin River. As discussed in more detail below, salmon runs on the main 

stem San Joaquin River upstream of the confluence with the Merced River are being restored 

pursuant to the San Joaquin River Restoration Settlement Act of 2009 (San Joaquin Restoration 

Act).332

The San Joaquin River basin downstream of the confluence of the mainstem San Joaquin 

River and the Merced River also support salmon populations. Fall-run chinook salmon, 

presently not listed under the ESA, are able to spawn below the major dams on each of the three 

main tributaries to the San Joaquin River (the Stanislaus, Tuolumne, and Merced rivers), but 

their abundance has declined sharply in the last 10 years.333 At present, only the Stanislaus River 

is believed to support a population of steelhead, listed as threatened since 1998. Migratory 

survival measured for salmon through the southern Delta is poor compared to survival of 

Sacramento River outmigrants, and juvenile survival since 2000 has been on a steady and steep 

decline, see Figure G.

334

 Although information about steelhead in the San Joaquin system is 

limited, the available information suggests a significant decline.

5. What information is available on the effects of salinity management on terrestrial plant 

communities and/or tidal marsh endemic species? What indirect effect does this have on 

aquatic communities?

6. Does the geographic location of low-salinity habitat have an effect on the quality of the 

habitat or its availability to species of concern? If so, what is the nature and extent of such 

effect? Is the distribution pattern of low salinity habitat important in determining its quality?

7. Are spring/neap differences in tidal water quality important for aquatic species? If so, 

how should these habitat characteristics be evaluated?

8. How can performance measures for species population and/or habitat condition be used to 

evaluate restoration of Bay Delta Estuary water quality?
58

Figure G. Estimated natural production of chinook salmon in the San Joaquin River335

Survival of salmonids migrating between the San Joaquin River basin and the Bay Delta 

Estuary is likely affected by many stressors, including high predation rates, high temperatures, 

low dissolved oxygen, agricultural contaminants, urban stormwater impacts, diversion into local 

agricultural diversions and the state and federal export facilities that pump water south of the 

Delta for agricultural and urban consumption. Migration of salmonids is broadly believed to be 

guided by multiple cues – particular physical or chemical characteristics of the natal stream or 

migratory corridor that trigger or enable migration. Recent research suggests that, because most 

San Joaquin River water was diverted either upstream or as it enters the Delta, in almost all 

months of almost all years approximately 40 kilometers of San Joaquin River channels in the 

delta contain almost exclusively water derived from the Sacramento River.336 The 40-kilometer 

discontinuity of non-natal water in the Bay Delta Estuary between the San Joaquin River and the 

ocean suggests that salmon and steelhead migratory abilities may be severely compromised due 

to the absence of the necessary physical or chemical cues usually found in the natal waters or 

particular migration corridors. The absence of these characteristics may compromise migration 

independent of the effects of predation, temperature, oxygen depletion, contaminants and 

diversion. 

Retrospective analysis337 of earlier sonic tagging data338 found significant impairment of 

adult salmon migration to San Joaquin tributaries when total state and federal exports exceeded 

three times the volume of water entering from the San Joaquin River at Vernalis.339 Prior to the 

drought of 1987-1992, ratios greater than 3:1 were uncommon, while during the drought such 

conditions occurred almost every year. Between 1992 and 2001, such conditions varied from 

year to year based on hydrology, with ratios above and below 3:1. However, October conditions 

(the center of the fall migration period) from 2001 to 2008 have exceeded the 3:1 ratio in all but 

two years (see Figure H). As expected from the results of this research, returning numbers of 

salmon have been very low in all recent years.

0 

20000 

40000 

60000 

80000 

100000 

120000 

140000 

19521955195819611964196719701973197619791982198519881991199419972000200320062009
59

Figure H. Ratio of average combined CVP and SWP exports in October to monthly average October inflows of the San 

Joaquin River into the Delta.340 Ratios less than 3 were associated with successful migration of adult salmon to San 

Joaquin River Tributaries.341

b. Regulatory Status

The lower San Joaquin River and its major tributaries all include “Migration of Aquatic 

Species” as a designated use protected under the Clean Water Act.342 The State Board, in its 

1995 Water Quality Control Plan (unchanged in the 2006 revision), includes narrative criteria to 

protect the “Migration of Aquatic Species” designated use in the San Joaquin Basin.343 The 

narrative criteria establish a goal of doubling natural salmon production on the tributary streams 

of the Central Valley consistent with the federal goal embodied in the Central Valley Project 

Improvement Act of 1992. The Basin Plans implementing these narrative criteria have usually 

included a combination of changes to flows, diversions rates and gate manipulations to protect 

fish migration corridors, with emphasis on juvenile salmon outmigration in the February through 

June period. Since the mid-1990’s, the primary implementation mechanism of the narrative 

salmon criteria with respect to fall run salmon has been through the Vernalis Adaptive 

Management Plan (VAMP). The VAMP is a fixed-term, multi-year experiment designed to 

evaluate salmon migration success under different combinations of San Joaquin River inflows at 

Vernalis and CVP/SWP export restrictions. The VAMP experiment is drawing to a close, and 

the State Board is considering replacement implementation approaches based in part on the 

results of the VAMP. 

The Water Boards have adopted numeric criteria to address low dissolved oxygen in 

Delta waters.344 Since at least the 1970’s, blockage of adult salmonid migration due to low 

dissolved oxygen has received much scientific attention. Dissolved oxygen barriers occur in the 

Stockton Deep Water Ship Channel on the lower San Joaquin River and on Old and Middle 

Rivers. A TMDL for dissolved oxygen in the Ship Channel was adopted by the Central Valley 

RWQCB on January 27, 2005 and approved by EPA on February 27, 2007.345 The TMDL 

includes a phased control program to reduce the amount of oxygen-demanding substances and 

their precursors. Early steps in implementing this TMDL include adoption of source controls 

from the outfall from the City of Stockton wastewater treatment plant and implementation of 

aeration facilities at the Port of Stockton. Longer term changes in channel form are also 

proposed for action by the Corps, and studies are required both upstream and downstream on the 
60

sources and impacts of oxygen depletion.346

Chinook salmon and steelhead have specific temperature tolerances during various lifestages, including both juvenile and adult migration. Temperature conditions at various life 

stages may currently be the limiting factor for successful recruitment.347 The Central Valley 

RWQCB Basin Plan includes narrative and numeric criteria protecting, among others, the 

migratory aquatic organisms designated use.348 Recently, CDFG recommended that the Central 

Valley RWQCB list the San Joaquin and its tributaries as impaired waterbodies under the Clean 

Water Act for coldwater fisheries due to high water temperature. CDFG data show that EPA 

temperature guidance criteria for protecting salmon are frequently exceeded for all life stages.349 

In particular, CDFG has found that temperatures in the San Joaquin, Stanislaus, Tuolumne, and 

Merced Rivers exceeded EPA's adult chinook migration criterion (18 degrees) for 33% to 75% 

of the migration season, and for certain reaches, exceeded the criterion for juvenile migration for 

more than 50% of the season. The State Board declined to list the San Joaquin River and its 

tributaries as impaired due to elevated temperature, but EPA, in its review of the 303(d) list, 

added this listing when it acted on the State Board’s submission.350 Listing these water bodies as 

impaired is also supported by NMFS, who cite warm water temperatures below Central Valley 

dams as one of four major factors contributing to the decline of listed salmonids.351

The State Board has initiated a comprehensive reevaluation of San Joaquin River Flow 

and Southern Delta Salinity Objectives and a program of implementation to achieve these 

objectives. A staff report on the scientific basis for objectives was released in October 2010,352

and final action on any changes is currently scheduled for 2012.353 These objectives protect a 

suite of designated uses. With respect to fish and wildlife designated use protection (including 

salmonids), the report concludes that “a higher and more naturally variable inflow regime from 

the [San Joaquin River] to the Delta during the spring period (February through June) is 

needed.”354 

Pursuant to recent state law, the State Board recently issued recommendations on the 

flow necessary to protect public trust resources in the Bay Delta Estuary. This report identifies 

the need for an October pulse flow of 3600 cubic feet per second for a minimum of ten days on 

the San Joaquin River and concurrent reduction in exports to ensure a hydraulic connection 

between the River and the San Francisco Bay to allow adult salmon upmigration.355 These 

recommendations were identified in the report as “Class A,” meaning there was more robust 

scientific information to support specific numeric criteria than some other recommendations. 

The report notes that this recommendation is based on the needs of fall-run salmon and that 

similar flow needs for migrating adult steelhead are largely unknown.

The 2009 NMFS Biological Opinion on the effects of SWP and CVP project operations 

included requirements specifically addressing the needs of San Joaquin steelhead.356 Steelhead 

migrate during the same timeframe as fall-run salmon and are thought to respond similarly to 

environmental conditions. The NMFS Biological Opinion requires attraction flows in October of 

1500 cubic feet per second from Goodwin Dam on the Stanislaus River.357 No steelhead 

protection measures were included in the Delta for the adult migration season, September to 

November, largely because there is little information on steelhead migration and fall-run salmon 

are probably a poor surrogate.358 The ability of steelhead juveniles to hold over in their natal 
61

streams for more than one year may buffer them from some of the effects suffered by fall-run 

salmon.

The San Joaquin River Restoration Act359 is a federal commitment to restoring chinook 

salmon on the San Joaquin River. The legislation implements a court settlement reached in 2007 

amongst the USBR, the water contractors, and certain environmental groups. Under the 

settlement, specific physical restoration actions to reestablish the river channel and sufficient 

river flows will occur on the San Joaquin River in conjunction with reintroduction of spring-run 

salmon by December 31, 2012. The San Joaquin Restoration Act is focused on activities and 

habitat upstream of the confluence of the San Joaquin and Merced Rivers. The measured 

survival360 and decreasing populations of salmon in the San Joaquin watershed suggest that fallrun salmon restoration to the San Joaquin River tributaries cannot succeed until the lower 

migratory corridor is more supportive of salmon migration. Much attention has focused on the 

outmigration of young fish, but there is reason for concern that adults are not able to migrate 

upstream. 

c. Request for Public Comment

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information with citations that support your comments.

1. What role, if any, do gradients in physical and chemical constituents of water play in the 

suitability of the Bay Delta Estuary and San Joaquin River Basin migratory corridor for 

salmon?

2. What are the best measures of success for restoration of a migratory corridor? Could these 

measures be incorporated into new or revised biological criteria protecting the fish migration 

designated use? 

3. Should temporal characteristics be included in the definition of the physical and/or 

chemical properties of a migration corridor based on a reference condition? If so, how? What 

frequency and duration of such a corridor is required for salmonids? How might these 

characteristics change with the impacts of climate change?
62

3. Wetlands

a. Aquatic Resource Issues

The extensive historical destruction of the Bay Delta Estuary’s wetland and riparian areas 

increases the importance of the remaining wetland, riparian, and slough resources and the 

services they perform for Bay Delta water quality and flood protection. Over 95% of the 

historical 350,000 acres of tidal wetlands, sloughs, and riparian areas have been eliminated in the 

Bay Delta Estuary.361 Wetlands, sloughs, and riparian areas in the upper watersheds of the 

Sacramento and San Joaquin River basins experienced a similar reduction in areal extent.362 The 

elimination of these aquatic resources destroyed natural pollution filtration services (e.g., 

sediment, nitrogen, phosphorus, heavy metals)363 and flood protection functions that protected 

the Bay Delta Estuary.

b. Regulatory Status

The Clean Water Act Section 404 Program is a significant component of the Clean Water 

Act regulatory framework in the Bay Delta Estuary. The California State Reclamation Board 

estimates that approximately 130,000 new homes364 are at various stages of planning and 

implementation within the Bay Delta Estuary, potentially converting up to 55,000 acres365 of 

tracts and islands that are near or below sea level to urban landscape. Other potential large 

projects that could result in the discharge of dredge or fill material to protected waters include 

building a new conveyance through or around the Delta to divert water from the Sacramento 

River south to the export facilities in the southern Delta, dredging of the Sacramento and 

Stockton (San Joaquin) deepwater ship channels, tidal barrier projects, large-scale restoration 

activities, and a large-scale (22,000 acres) water storage project. This ANPR is not meant to 

suggest a decision or commitment to undertake any of these types of projects. Any such projects 

would need to go through all appropriate planning and decision-making processes before such a 

commitment is made.

These potential large projects may require Clean Water Act Section 404 permits, and 

some have the capability to negatively impact water quality in the Bay Delta Estuary. While 

potentially improving export water quality and reducing fish entrainment at the south Delta 

export facilities, any conveyance project that diverts relatively clean Sacramento River water 

4. Would establishing a migratory corridor for upmigrating adult chinook salmon succeed in 

improving adult migration success if temperatures in the river channels upstream of Vernalis 

are unchanged? If so, how? How might actions to establish a migratory corridor in the south 

Delta also moderate temperature and/or dissolved oxygen problems in the San Joaquin River? 

5. Are additional efforts to improve dissolved oxygen regimes in the Delta necessary to 

provide an adequate migratory corridor for San Joaquin salmonids? If so, what should those 

efforts include?

6. What other information is available on barriers to salmon migration in the Bay Delta 

Estuary and San Joaquin River watershed?
63

before it enters the Bay Delta Estuary also has the potential to exacerbate existing water 

pollutions problems (such as increased salinity and low dissolved oxygen) in the Bay Delta 

Estuary. Dredging operations have the potential to re-suspend sediments and contaminants, 

thereby contributing to existing water quality impairments. Tidal barrier and storage projects 

have the potential to reduce circulations in areas of the Estuary that suffer from salinity and low 

dissolved oxygen impairments. 

Urban development of Bay Delta Estuary rural islands and tracts eliminates the ability of 

these areas to retain and assimilate sediment and associated contaminants and store and absorb 

flood waters. Statewide, salt marsh and riverine wetlands are showing declining function as a 

result of urbanization.366 Conversion of agricultural land use to urban land use on these islands 

and tracts may also adversely impact water quality as higher urban stormwater and POTW 

discharges increase the volume and array of pesticides and contaminants discharged into the 

adjacent waterways. 

c. Request for Public Comment

Many activities discussed in this notice are already the subject of a formal or informal 

rulemaking process conducted by either EPA or a related state or federal agency. Nothing in this 

notice is intended to supersede those ongoing processes, nor does this notice constitute a decision 

under any of those processes. If commenters have submitted material in connection with those 

other processes that is believed to be relevant to the issues raised in this notice, the commenter 

may either reference the earlier submission (if it was submitted to EPA), attach the earlier 

submission (if it was submitted to a different agency), or, if appropriate, provide a link to the 

material online.

Please provide the reason(s) for answers to the following questions and scientific, policy, 

and/or legal information with citations that support your comments.

1. What different approaches under the Clean Water Act Section 404 program should EPA 

consider, in consultation with the U.S. Army Corps of Engineers, to improve the protection of 

aquatic resource functions in the Bay Delta Estuary? 

2. What information exists that describes the relationship between the quantity and quality of 

wetlands and Bay Delta Estuary water quality and fish populations?

3. In light of projected impacts of climate change (including sea level rise and its effects on 

levee stability), what specific activities can EPA undertake to improve long-term protection of 

existing and future wetlands, especially those resources on subsided islands?
64

IV. EXECUTIVE ORDER 12866, Regulatory Planning and Review

Under Executive Order 12866, entitled Regulatory Planning and Review (58 Federal 

Register 51,735, October 4, 1993), this is a “significant regulatory action.” Accordingly, EPA 

submitted this action to the Office of Management and Budget (OMB) for review under 

Executive Order 12866 and any changes made in response to OMB recommendations have been 

documented in the docket for this action. 

Because this action does not propose or impose any requirements and instead seeks 

comments and suggestions for the Agency to consider in possibly developing a subsequent 

proposed rule, the various statutes and Executive Orders that normally apply to rulemaking do 

not apply in this case. Should EPA subsequently determine to pursue a rulemaking, EPA will 

address the statutes and Executive Orders applicable to that rulemaking. 

Dated: February 10, 2011

(original signed by)

Jared Blumenfeld

Regional Administrator, U.S. Environmental Protection Agency, Region 9
65

 

V. ENDNOTES

1 There is no commonly accepted precise geographic definition of the Bay Delta Estuary. The “legal Delta” is welldefined for purposes of the California Delta Protection Commission and related California statutes, but is not coterminous with the functioning estuary. This ANPR will generally refer to the larger estuary upstream of the San 

Francisco Bay as the Bay Delta Estuary or the Estuary. It will also refer to the Delta, which usually means the 

“legal Delta” plus Suisun Marsh and Suisun Bay. Occasionally, this ANPR may also reference the Bay Delta 

Estuary watershed, which is a huge land area that includes the drainages of the Sacramento and San Joaquin River 

basins. 

2 Clean Water Act, 33 U.S.C. §§ 1281-1387 (2006).

3

“Anadromous” species are those, such as chinook salmon and steelhead, that spend at least some of their life cycle 

in salt water. Usually, these species return to freshwater to spawn.

4 Water years in California are defined as October 1 through the following September 30. For example, the 2011 

water year began October 1, 2010 and continues through September 30, 2011. Water years in California are 

categorized based on the particular rainfall that year. The categories are wet, above normal, below normal, dry, and 

critically dry.

5 Endangered Species Act, 16 U.S.C. §§ 1531-1544 (2006).

6

See CAL. DEP’T OF WATER RES. & BUREAU OF RECLAMATION, WATER SUPPLY CONDITIONS 2009 (Aug., 2009), 

available at http://www.water.ca.gov/news/newsreleases/2009/08122009martinmilligan2.pdf (suggests that 

approximately a quarter (500 thousand acre feet) of the 2.1 million acre feet water export shortfall in 2009 was due 

to new environmental restrictions, whereas three quarters (1.6 million acre feet) of the shortfall was due to the 

drought itself). 

7

See Press Release, U.S. Dep’t of the Interior, Secretary Salazar, Senior Administration and Congressional Officials 

Hold Town Hall Meeting on California Water Shortage (June 28, 2009), available at

http://www.doi.gov/news/pressreleases/2009_06_28_release.cfm (discussing several water augmentation initiatives).

8 California Bay-Delta Memorandum of Understanding among Federal Agencies (Sept. 29, 2009), available at

http://www.doi.gov/documents/BayDeltaMOUSigned.pdf.

9

INTERIM FEDERAL ACTION PLAN FOR THE CALIFORNIA BAY-DELTA (Dec. 22, 2009), available at

http://www.doi.gov/documents/CAWaterWorkPlan.pdf.

10 Citations to these many reports and reviews are provided below, as each issue is discussed in detail.

11 RANDALL BAXTER, ET AL., PELAGIC ORGANISM DECLINE PROGRESS REPORT: 2010 SYNTHESIS OF RESULTS (2010),

available at http://www.water.ca.gov/iep/docs/FinalPOD2010Workplan12610.pdf.

12 The State Board, Central Valley RWQCB, and San Francisco Regional Water Quality Control Board (San 

Francisco RWQCB) will sometimes be referred to collectively as the “Water Boards.”

13 As noted in more detail below, much of EPA’s statutory mandate is to perform oversight and review of state water 

quality agency activities.

14 Federal Insecticide, Fungicide and Rodenticide Act, 7 U.S.C. § 136-136y (2006).

15 STATE WATER RES. CONTROL BD., CENT. VALLEY WATER BD., & SAN FRANCISCO BAY WATER BD., STRATEGIC 

WORKPLAN FOR ACTIVITIES IN THE SAN FRANCISCO BAY/SACRAMENTO-SAN JOAQUIN DELTA ESTUARY (2008), 

available at 

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/strategic_plan/docs/baydelta_workpla

n_final.pdf. 

16 National Environmental Policy Act, 42 U.S.C. § 4321-4370f (2006).

17 Natural Community Conservation Plan Act, CAL. FISH & GAME CODE § 2800-2835 (2003).

18 Although the scope of the BDCP covers at least nine listed aquatic species and a geographic area of over one-half 

million acres, the BDCP is not intended to be a comprehensive Delta recovery plan. By its own terms, it is 

intended to meet ESA requirements by addressing only the operations of the state and federal water export projects 

and their impacts on listed species and their habitat. 

19 CAL. WATER CODE § 85300-85350 (2010).

20 Letter from Delta Independent Science Board to Phil Isenberg, Chair, Delta Stewardship Council (Jan. 26, 2011), 

available at http://www.deltacouncil.ca.gov/delta_science_program/pdf/isb/disb_20110126_stressor_short_memo_final.pdf.

21 DELTA VISION BLUE RIBBON TASK FORCE, DELTA VISION STRATEGIC PLAN (Oct. 2008), available at

http://deltavision.ca.gov/StrategicPlanningProcess/StaffDraft/Delta_Vision_Strategic_Plan_standard_resolution.pdf; 
66

 

Estimate of federal and state endangered and threatened species based on discussion with U.S. Fish & Wildlife 

Service biologists; BAY DELTA CONSERVATION PLAN, STEERING COMMITTEE WORKING DRAFT (Nov. 18, 2010), 

available at

http://baydeltaconservationplan.com/Libraries/Whats_in_Plan/draft_BDCPreport_11292010_ClickableLinks7.pdf; 

CALFED BAY DELTA PROGRAM, MULTI-SPECIES CONSERVATION STRATEGY, FINAL PROGRAMMATIC EIS (July 7, 

2000), available at http://dfg.ca.gov/erp/envcomp_mscs.asp.

22 Anti-Deficiency Act, 31 U.S.C. § 1341 (2007).

23 JAY LUND ET AL., ENVISIONING FUTURES FOR THE SACRAMENTO-SAN JOAQUIN DELTA (Feb. 2007), available at 

http://www.ppic.org/main/publication.asp?i=671; See DELTA VISION BLUE RIBBON TASK FORCE, OUR VISION FOR 

THE CALIFORNIA DELTA (Jan. 2008), available at

http://deltavision.ca.gov/BlueRibbonTaskForce/FinalVision/Delta_Vision_Final.pdf (The current status and future 

threats to the Estuary have been well documented. Good summaries of these issues can be found in these sources).

24 JOHN E. SKINNER, AN HISTORICAL REVIEW OF THE FISH AND WILDLIFE RESOURCES OF THE SAN FRANCISCO BAY 

AREA 226 (Cal. Dept. of Fish and Game, Water Projects Branch Rep. No. 1, 1962), available at

http://www.estuaryarchive.org/archive/skinner_1962/; W.A. Bennett & Peter Moyle, Where Have All the Fishes 

Gone? Interactive Factors Producing Fish Declines in the Sacramento-San Joaquin Estuary, in SAN FRANCISCO 

BAY: THE ECOSYSTEM 519, 519-42 (J.T. Hollibaugh ed., 1996); PETER MOYLE ET AL., 2010 CHANGING 

ECOSYSTEMS: A BRIEF ECOLOGICAL HISTORY OF THE DELTA (Feb. 2010), available at

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/docs/intro_delta_history_14

feb2010.pdf. 

25 Ted Sommer, et al., The Collapse of Pelagic Fishes in the Upper San Francisco Estuary, 32 FISHERIES, n.6, 270,

270-77 (2007) (Graphs originally prepared for Ted Sommer, et al., updated for 2008 and 2009 with data from Cal. 

Dep’t of Fish & Game, http://www.dfg.ca.gov/delta/projects.asp?ProjectID=FMWT (last visited Nov. 16, 2010)).

26 Fall run chinook salmon is also an important food source for the southern population of killer whales, which are 

listed as threatened under the ESA.

27 Since harvest data are a large part of the population estimation tool, data for these three years are probably not 

directly comparable with earlier yearly population estimates.

28 S.T. LINDLEY ET AL., WHAT CAUSED THE SACRAMENTO RIVER FALL CHINOOK STOCK COLLAPSE? (2009), 

available at http://swr.nmfs.noaa.gov/media/SalmonDeclineReport.pdf.

29 Id.

30 Sommer et al., supra note 25; Alan Jassby & T.M. Powell, Hydrodynamic Influences on Interannual Chlorophyll 

Variability in an Estuary: Upper San Francisco Bay Delta, 39 ESTUARINE, COASTAL & SHELF SCI. 595, 595-618 

(1994); W.J. Kimmerer, Effects of Freshwater Flow on Abundance of Estuarine Organisms: Physical Effects or 

Trophic Linkages?, 243 MARINE ECOLOGY PROGRESS SERIES 39, 39-55 (2002).

31 James R. Thomson et al., Bayesian Change-Point Analysis of Abundance Trends for Pelagic Fishes in the Upper 

San Francisco Estuary, 20 ECOLOGICAL APPLICATIONS 1431, 1431-48 (2010); Ralph Mac Nally et al., An Analysis 

of Pelagic Species Decline in the Upper San Francisco Estuary using Multivariate Autoregressive Modeling (MAR),

20 ECOLOGICAL APPLICATIONS, 167, 167-80 (2010).

32 The Fall Midwater Trawl is an ongoing annual survey of pelagic species abundance conducted by the California 

Department of Fish and Game. Some of the numbers in the 1970’s are not comparable because the survey was not 

conducted in 1974, 1976 or in part of the fall of 1978. Therefore, the entries on the chart represent “no data.” In 

addition, the index for longfin smelt shows substantial variation over the period, and graph presents only the lower 

quartile of the actual range of index numbers. 

33 The IEP is a consortium of nine state and federal agencies plus the San Francisco Estuary Institute. Since the 

1970’s, it has, primarily through its member entities, collected and analyzed data on water quality, fish, wildlife and 

related hydrodynamic processes in the Bay Delta Estuary. 

34 BAXTER ET AL., supra note 11; RANDALL BAXTER, ET AL., PELAGIC ORGANISM DECLINE PROGRESS REPORT: 2007

SYNTHESIS OF RESULTS (2008), available at http://www.science.calwater.ca.gov/pdf/workshops/POD/2007_IEPPOD_synthesis_report_031408.pdf; CHUCK ARMOR, ET. AL, INTERAGENCY ECOLOGICAL PROGRAM SYNTHESIS OF 

2005 WORK TO EVALUATE THE PELAGIC ORGANISM DECLINE IN THE UPPER SAN FRANCISCO ESTUARY (2005).

35 Lenny F. Grimaldo, et al., Factors Affecting Fish Entrainment into Massive Water Diversions in a Tidal 

Freshwater Estuary: Can Fish Losses be Managed?, 29 N. AM. J. OF FISHERIES MGMT. 1253, 1253-70 (2009). 

36 Id. Entrainment refers to the diversion and probable loss of fish at the export facilities.

37 Frederick Feyrer, M.L. Nobriga & T.R. Sommer, Multi-Decadal Trends for Three Declining Fish Species: 
67

 

Habitat Patterns and Mechanisms in the San Francisco Estuary, California USA, 64 CAN. J. OF FISHERIES &

AQUATIC SCI. 723, 723-34 (2007).

38 William Bennett, Critical Assessment of the Delta Smelt Population in the San Francisco Estuary, California, 3 

SAN FRANCISCO ESTUARY & WATERSHED SCI. 1, 1-70 (2005), available at 

http://repositories.cdlib.org/jmie/sfews/vol3/iss2/art1; M.L. Nobriga & B. Herbold, The Little Fish in California’s 

Water Supply: a Literature Review and Life-History Conceptual Model for Delta Smelt (Hypomesus transpacificus) 

for the Delta Regional Ecosystem Restoration and Implementation Plan (DRERIP) (2010) (in review)(on file with 

authors); Frederick Feyrer, T. Sommer & S.B. Slater, Old School vs. New School: Status of Threadfin Shad 

(Dorosomapetenense) Five Decades After its Introduction to the Sacramento-San Joaquin Delta, 7 SAN FRANCISCO 

ESTUARY & WATERSHED SCI. 1, 1-17 (2009), available at http://repositories.cdlib.org/jmie/sfews/vol7/iss1/art3.

39 LINDLEY ET AL., supra note 22; JAY R. LUND ET AL., PUB. POLICY INST. OF CAL., COMPARING FUTURES FOR THE 

SACRAMENTO-SAN JOAQUIN DELTA (2008), available at www.ppic.org/content/pubs/report/r_708EHR.pdf.

40 James Cloern et al., Biological Communities in San Francisco Bay Track a North Pacific Climate Shift, 37 

GEOPHYSICAL RES. LETTERS 1, 1-6 (2010).

41 Agency for Toxic Substances & Disease Registry (ATSDR), Fact Sheet: Pyrethrins and Pyrethroids (2003), 

available at http://www.atsdr.cdc.gov/tfacts155.pdf ("Pyrethroids are manufactured chemicals that are very similar 

in structure to the pyrethrins, but are often more toxic to insects as well as to mammals, and last longer in the 

environment than the pyrethrins....Pyrethrins are naturally-occurring compounds with insecticidal properties that are 

found in pyrethrum extract from certain chrysanthemum flowers"). 

42 W.A. BENNETT, J.A. HOBBS & S.J. TEH, INTERPLAY OF ENVIRONMENTAL FORCING AND GROWTH-SELECTIVE 

MORTALITY IN THE POOR YEAR-CLASS SUCCESS OF DELTA SMELT IN 2005 (2008), available at

http://www.science.calwater.ca.gov/pdf/workshops/POD/2008_final/Bennett_PODDeltaSmelt2005Report_2008 

.pdf.

43 Some pyrethroid insecticides are toxic to invertebrates, which are food for pelagic fish, at or near the low 

“detection level.” The “detection level” is the concentration at which feasible test methods can detect the presence 

of a constituent. 

44 Kathryn Kuivila & G.E. Moon, Potential Exposure of Larval and Juvenile Delta Smelt to Dissolved Pesticides in 

the Sacramento-San Joaquin Delta, California, 39 AM. FISHERIES SOC’Y SYMP. 229, 229-42 (2004).

45 Weston et al., Distribution and Toxicity of Sediment-Associated Pesticides in Agriculture-Dominated Water 

Bodies of California’s Central Valley, 38 ENVTL. SCI. & TECH. 2752, 2752-59 (2004).

46 Richard C. Dugdale, F.P. Wilkerson, V.E. Hogue & A., Marchi, The Role of Ammonium and Nitrate in Spring 

Bloom Development in San Francisco Bay, 73 ESTUARINE, COASTAL & SHELF SCI. 17, 17-29 (2007).

47 Erin Lee Hestir, D. Schoellhammer, T. Morgan & S.L. Ustin, Trends in Submerged Aquatic Vegetation and 

Turbidity in the Sacramento-San Joaquin Delta, Presentation at the 5th Biennial CALFED Science Conference (Oct. 

22-24, 2008); M.J. Santos, L.W. Anderson & S.L. Ustin, Effects of Invasive Species on Plant Communities: An 

Example Using Submersed Aquatic Plants at the Regional Scale, BIOLOGICAL INVASIONS 1, 1-15 (Jul. 28, 2010), 

available at http://www.springerlink.com/content/b883gr221203xr37/ (Despite these treatments, the area occupied 

by submerged aquatic vegetation continues to spread at an average annual rate of 13%. In recent years treatment has 

focused solely on Franks Tract for aquatic vegetation control and has been successful in that locale).

48 M.F.L.L Lurling & I. Roessink, On the Way to Cyanobacterial Blooms: Impact of the Herbicide Metribuzin on the 

Competition Between a Green Alga (Scenedesmus) and a Cyanobacterium (Microsystis), 65 CHEMOSPHERE 618, 

618-26 (2006); Hans Paerl, Nutrient and Other Environmental Controls of Harmful Cyanobacterial Blooms Along 

the Freshwater-Marine Continuum in Cyanobacterial Harmful Algal Blooms: State of the Science and Research 

Needs, 619 ADVANCES IN EXPERIMENTAL MED. & BIOLOGY 217, 217-37 (2008). 

49 Patricia M. Glibert, Long-term Changes in Nutrient Loading and Stoichiometry and their Relationships with 

Changes in the Food Web and Dominant Pelagic Fish Species in the San Francisco Estuary, California, 18 

REVIEWS IN FISHERY SCI. 211, 211-32 (2010) (The existence of multiple interacting stressors can confound results of 

single-stressor research. For example, increased ammonia loading is linked to decreased diatom production); 

Kimmerer, supra note 30 (Equally consistent with the data is the establishment of overbite clams, increasing diatom 

consumption); James R. Thomson et al., Bayesian Change-Point Analysis of Abundance Trends for Pelagic Fishes 

in the Upper San Francisco Estuary, 20 ECOLOGICAL APPLICATIONS 1431, 1431-48 (2010) (Both factors are 

probably responsible for the decline in diatoms in the low salinity zone but both factors are also affected by 

hydrological changes: low river flows due to drought have likely increased the effects of ammonia loading while 

stabilized salinity regimes have allowed high densities of overbite clams to accrue in the western delta).
68

 

50 PETER MOYLE ET AL., DELTA SOLUTIONS CTR. FOR WATERSHED SCI., UNIV. OF CAL., DAVIS, HABITAT 

VARIABILITY AND COMPLEXITY IN THE UPPER SAN FRANCISCO ESTUARY (2010), available at 

http://deltasolutions.ucdavis.edu/pdf/WorkingPapers/HabitatVariabilityandComplexity-2010Draft.pdf; BROWN ET 

AL., IEP POD WORKPLAN 2010 (forthcoming 2010), available at http://calwater.ca.gov/science/pod/pod_index.html; 

James Cloern, Senior Research Scientist, U.S. Geological Survey, Historical Perspective on Human Disturbance in 

the Sacramento-San Joaquin Delta Ecosystem, Presentation at the National Research Council’s Meeting on 

Sustainable Water and Environmental Management in the California Bay-Delta (July 13, 2010); Anke MuellerSolger, IEP Lead Scientist Delta Stewardship Council, IEP Science Highlights, 2009-2010, Summary Presentation at 

IEP Annual Workshop (May 25, 2010), available at http://www.water.ca.gov/iep/docs/052510Science.pdf ; 

Thomson et al., supra note 49; Mac Nally et al., supra note 31.

51 Hestir, Schoellhammer, Morgan & Ustin, supra note 47; Santos, Anderson & Ustin, supra note 47; Matthew L. 

Nobriga, T. Sommer, F. Feyrer & K. Fleming, Long-Term Trends in Summertime Habitat Suitability for Delta Smelt 

(Hypomesus transpacificus), 6 SAN FRANCISCO ESTUARY & WATERSHED SCI. 1, 1 n.1 (Feb. 2008), available at

http://repositories.cdlib.org/jmie/sfews/vol6/iss1/art1.

52 Peter B. Moyle & W.A. Bennett, The Future of the Delta Ecosystem and its Fish, in COMPARING FUTURES FOR 

THE SACRAMENTO-SAN JOAQUIN DELTA (TECHNICAL APPENDIX D) (Pub. Policy Inst. of Cal. ed., 2008), available at

http://www.ppic.org/content/pubs/other/708EHR_appendixD.pdf. 

53 LUND, supra note 23; Cloern supra note 50.

54 VIVIAN GADDIE, MICHAEL MIERZA & JENNY MARR, LEVEE FAILURES IN THE SACRAMENTO-SAN JOAQUIN RIVER 

DELTA, available at http://www.dwr.water.ca.gov/floodmgmt/docs/DeltaLeveeFailures_FMA_200709.pdf (last 

visited Nov. 3, 2010).

55 Letter from Phillip L. Isenberg, Chair, Delta Vision Blue Ribbon Task Force, to Arnold Schwarzenegger, 

Governor, Cal. (Mar. 24, 2008), available at

http://deltavision.ca.gov/BlueRibbonTaskForce/Communications/SLR_Followup_Letter_To_Governor_9-4-08.pdf. 

(The Governor’s Delta Vision Blue Ribbon Task Force estimated and adopted for its planning purposes a projected 

sea level rise of 55 inches by the year 2100).

56 CAL. DEPT. OF WATER RESOURCES, MANAGING AN UNCERTAIN FUTURE: CLIMATE CHANGE ADAPTATION 

STRATEGIES FOR CALIFORNIA’S WATER (Oct. 2008), available at

http://www.water.ca.gov/climatechange/docs/ClimateChangeWhitePaper.pdf.

57 Given that 20 million Californians get some or all of their drinking water from the Bay Delta Estuary, it may seem 

counterintuitive that EPA is not including the Public Health Service Act, 42 U.S.C. § 300f et seq. (2006) (generally 

referred to as the Safe Drinking Water Act) as one of the major statutes affecting Bay Delta Estuary aquatic 

resources. That Act, however, focuses on water quality “at the tap” and on the activities of public water supply 

agencies. Although the targeted drinking water parameters at the tap are a very relevant consideration in Bay Delta 

Estuary resource management, the regulatory tools for protecting sources of drinking water are found primarily in 

the Clean Water Act.

58 40 C.F.R. § 131.3(i) (Dec. 14, 1994) (Under EPA regulations, a water quality standard consists of a “designated 

use or uses for the waters of the United States and water quality criteria for such waters based upon such uses”). 

59 40 C.F.R. § 131.2 (Dec. 22, 1992) (Under EPA regulations, “Serve the purposes of the Act'' (as defined in 

Sections 101(a), 101(a)(2), and 303(c) of the Act) means that water quality standards should: (1) include provisions 

for restoring and maintaining chemical, physical, and biological integrity of state and tribal waters, (2) provide, 

wherever attainable, water quality for the protection and propagation of fish, shellfish, and wildlife and recreation in 

and on the water (“fishable/swimmable''), and (3) consider the use and value of state and tribal waters for public 

water supplies, propagation of fish and wildlife, recreation, agricultural and industrial purposes, and navigation).

60 The Central Valley RWQCB incorporates any final State Board criteria into their plans.

61 STATE WATER RES. CONTROL BD., WATER QUALITY CONTROL PLAN FOR THE SAN FRANCISCO 

BAY/SACRAMENTO-SAN JOAQUIN DELTA ESTUARY (Dec. 13, 2006), available at 

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/wq_control_plans/2006wqcp/docs/200

6_plan_final.pdf. 

62 33 U.S.C. § 1342(b)(1)(B) (2008).

63 33 U.S.C. § 1311 (a)-(b) (1995).

64 33 U.S.C. §§ 1311(b)(2) (1995), 1314(b) (2000), 1316 (1972), 1317(b)-(c) (1987).

65 33 U.S.C. §§ 1311(a)-(b) (1995), 1342 (2008). 

66 33 U.S.C. §§ 1317(b)-(c) (1987).
69

 

67 The major POTWs affecting the Estuary are listed in Section III.A.2. 

68 Water Board actions on these permit renewals are not solely the result of the POD issues. The Boards are 

required to look at a broad range of water quality issues in their permit decisions.

69 City of Stockton’s Waste Water Treatment Plant NPDES permit, Order No. R5-2002-0083 (2002).

70 Cease and Desist Order, Order No. R5-2002-0084 (2002).

71 55 Fed. Reg. 47990 (Nov. 16, 1990).

72 64 Fed. Reg. 68721 (Dec. 8, 1999).

73 See 33 U.S.C. § 402(p) (2000); 40 C.F.R. §122.26 (June 12, 2006).

74 40 C.F.R. § 122.26(b)(8) (June 12, 2006).

75 40 C.F.R. § 122.26(b)(16) (June 12, 2006).

76 See Water Quality Order, Order No. 2003-0005-DWQ (2003).

77 40 C.F.R. § 122.26(b)(14)(x) (June 12, 2006).

78 40 C.F.R. § 122.26(b)(15) (June 12, 2006).

79 California Construction General Permit, Order No. 2009-0009-DWQ (2009).

80 40 C.F.R. § 122.26(a)(9)(i)(C)-(D) (June 12, 2006). 

81 40 C.F.R. § 122.35 9 (Dec. 8, 1999).

82 33 U.S.C. § 1313(d)(1)(A) (2000).

83 40 C.F.R. § 130.7(b) (Mar. 19, 2003).

84 40 C.F.R. § 130.7(d)(1) (Mar. 19, 2003).

85 33 U.S.C. §1313(d)(2) (2000).

86 33 U.S.C. § 1313(d)(1)(C) (2000).

87 40 C.F.R. § 130.2(g)-(i) (Mar. 19, 2003). 

88 See Dioxin/Organochlorine Ctr. v. Clarke, 57 F.3d 1517, 1520 (9th Cir. 1995).

89 40 C.F.R. §130.7(c)(1)(ii) (Mar. 19, 2003) (In addition to the listing process for impaired waters described above, 

Section 303(d)(3) requires States to identify and estimate TMDLs for waters that are not impaired. Unlike TMDLs 

established under Section 303(d)(1), States are not required to submit TMDLs estimated pursuant to Section 

303(d)(3) to EPA. Information developed under Section 303(d)(3) may be used to protect waters to ensure they 

continue to meet WQS).

90 33 U.S.C. § 1313(d)(2) (2000).

91 33 U.S.C. § 1313(d)(2) (2000).

92 40 C.F.R. § 122.44(d)(1)(vii)(B) (Apr. 11, 2007); NRDC v. EPA, 915 F.2d 1316, 1316 (9th Cir. 1990). 

93 See NRDC, 915 F.2d at 1316 (noting that Clean Water Act does not “directly prohibit” release of pollutants from 

nonpoint sources).

94 STATE WATER RES. CONTROL BD., 2010 INTEGRATED REPORT CLEAN WATER ACT SECTIONS 303(D) AND 305(B)

(Apr. 19, 2010), available at http://www.waterboards.ca.gov/water_issues/programs/tmdl/integrated2010.shtml (On 

August 4, 2010, the State Water Resources Control Board reviewed and approved the 2010 Integrated Report, 

including the 303(d) listing); See Letter from Alexis Strauss, Water Div. Dir., U.S. EPA Region IX, to Tom Howard, 

Exec. Officer, State Water Res. Control Bd. (Nov. 12, 2010), available at

http://www.epa.gov/region9/water/tmdl/303d-pdf/EPAsPartial-Approval-Partial-DisapprovLtr-Enclos-Ca2008-

2010-303dList.pdf.

95 STATE WATER RES. CONTROL BD., CENT. VALLEY REG’L WATER QUALITY CONTROL BD. & SAN FRANCISCO BAY 

REG’L. WATER QUALITY CONTROL BD., supra note 15.

96 U.S. EPA Fact Sheet, Wetland Regulatory Authority, 

http://water.epa.gov/type/wetlands/outreach/upload/reg_authority_pr.pdf (last visited Nov. 3, 2010) (the Clean 

Water Act Section 404 program is conventionally referred to as the “Wetlands” program however, it applies to 

dredge and fill activities in all Clean Water Act jurisdictional waters. The types of waters that are jurisdictional 

under the Clean Water Act include, but are not limited to, streams, rivers, natural ponds, lakes, impoundments, 

estuaries, bays, ocean, mudflats, sloughs, and wetlands).

97 For example, fill activities that increase water velocity (armoring stream banks, straightening streams, piping 

streams in culverts) also increase the ability of moving water to entrain and carry sediment and other contaminants 

to downstream locations and decrease the likelihood that contaminants will settle out of the water column. Fill 

activities like boat dock construction may have minimal direct impact to an aquatic resource, but the increased boat 

activity has indirect negative water quality impacts from re-suspension of sediments, loss of subtidal vegetation, and 

combustion engine pollution. Dredging activities that require Clean Water Act Section 404 permits can also 
70

 

negatively affect water quality by digging up bottom sediments and suspending these sediments in the water column,

restricting light penetration to aquatic plants and reintroducing contaminants such as pesticides into sediments.

98 Clean Water Act 404(b)(1) Guidelines, 40 C.F.R. § 230.10 (Oct. 28, 2010).

99 U.S. EPA Fact Sheet, Functions and Values of Wetlands, 

http://water.epa.gov/type/wetlands/upload/2006_08_11_wetlands_fun_val.pdf (last visited Nov. 3, 2010).

100 Pesticides; Procedural Regulations for Registration Review, 71 Fed. Reg. 45719 (Aug. 9, 2006); 40 C.F.R. pt. 

155 subpt. C (Aug. 9, 2006). 

101 The National Research Council panel currently evaluating several Bay Delta Estuary science issues may be 

“ranking” factors associated with the decline of ESA listed species and other at-risk species. That ranking and the 

associated report is not due until 2011. Similarly, the Delta Independent Science Board has initiated a process to 

evaluate and rank the relative importance of multiple stressors and, especially, to consider the interactive effects of 

these multiple stressors. See DELTA STRESSORS WORKSHOP, MEETING NOTICE (Dec. 30, 2010), available at

http://www.deltacouncil.ca.gov/delta_science_program/pdf/isb/disb_2011_01_workshop_stressors_mtg_notice_122810.pdf.

102 STATE WATER RES. CONTROL BD., supra note 94.

103 Clean Water Act, 33 U.S.C. § 1362(13) (2006) (“The term ‘toxic pollutant’ means those pollutants, or 

combinations of pollutants, including disease-causing agents, which after discharge and upon exposure, ingestion, 

inhalation or assimilation into any organism, either directly from the environment or indirectly by ingestion through 

food chains, will, on the basis of information available to the Administrator, cause death, disease, behavioral 

abnormalities, cancer, genetic mutations, physiological malfunctions (including malfunctions in reproduction) or 

physical deformations, in such organisms or their offspring”).

104 MICHAEL L. JOHNSON ET AL., EVALUATION OF CHEMICAL, TOXICOLOGICAL, AND HISTOPATHOLOGICAL DATA TO 

DETERMINE THEIR ROLE IN THE PELAGIC ORGANISM DECLINE, (Apr. 20, 2010), available at 

http://www.swrcb.ca.gov/rwqcb5/water_issues/delta_water_quality/comprehensive_monitoring_program/contamina

nt_synthesis_report.pdf.

105 Glibert, supra note 49.

106 Erin L. Amweg, Donald P. Weston, Jing You & Michael J. Lydy, Pyrethroid Insecticides and Sediment Toxicity 

in Urban Creeks from California and Tennessee, 40 ENVTL. SCI. TECH. 1700, 1700–06 (2006).

107 DAVID OSTRACH ET AL., THE ROLE OF CONTAMINANTS, WITHIN THE CONTEXT OF MULTIPLE STRESSORS, IN THE 

COLLAPSE OF THE STRIPED BASS POPULATION IN THE SAN FRANCISCO ESTUARY AND ITS WATERSHED (2009), 

available at 

http://www.science.calwater.ca.gov/pdf/workshops/POD/POD_yr2_Ostrach_090522_report_final_djo.pdf.

108 U.S. ENVTL. PROT. AGENCY, 1999 UPDATE OF AMBIENT WATER QUALITY CRITERIA FOR AMMONIA (1999), 

available at

http://www.epa.gov/waterscience/standards/ammonia/99update.pdf.

109 David John Randall & T.K.N. Tsui, Ammonia Toxicity in Fish, 45 MARINE POLLUTION BULLETIN 17, 17-23 

(2002). 

110 U.S. ENVTL. PROT. AGENCY, DRAFT 2009 UPDATE AQUATIC LIFE AMBIENT WATER QUALITY CRITERIA FOR 

AMMONIA – FRESHWATER (2009), available at

http://water.epa.gov/scitech/swguidance/waterquality/standards/criteria/aqlife/pollutants/ammonia/upload/2009_12_

23_criteria_ammonia_2009update.pdf; U.S. ENVTL. PROT. AGENCY, supra note 108.

111 U.S. ENVTL. PROT. AGENCY, supra note 108.

112 IDA FLORES AT AL., ACUTE AND CHRONIC TOXICITY OF AMMONIA ON PSEUDODIAPTOMUS FORBESI (2010), 

available at http://www.water.ca.gov/iep/docs/052510LesmeisterB.pdf.

113 Randall & Tsui, supra note 109.

114 Ruth Francis-Floyd, Craig Watson, Denise Petty & Deborah B. Poude, Ammonia in Aquatic Systems, UNIV.OF 

FLA. IFAS EXTENSION, FA16 (2009), available at http://edis.ifas.ufl.edu/fa031.

115 U.S. EPA, National Nutrient Strategy, http://www.epa.gov/waterscience/criteria/nutrient/strategy/index.html (last 

visited Oct. 18, 2010).

116 Alan Jassby, Phytoplankton in the Upper San Francisco Estuary: Recent Biomass Trends, their Causes, and their 

Trophic Significance, 6 SAN FRANCISCO ESTUARY & WATERSHED SCI. 1 (Feb. 2008), available at 

http://escholarship.org/uc/item/71h077r1.

117 Id.; Frances P. Wilkerson et al., Phytoplankton Blooms and Nitrogen Productivity in the San Francisco Bay, 

29(3) ESTUARIES & COASTS 401, 401-16 (2006). 
71

 

118 Central Valley Regional Water Quality Control Board, Ammonia Summit Summary (Aug. 18-19, 2009), 

http://www.swrcb.ca.gov/rwqcb5/water_issues/delta_water_quality/ambient_ammonia_concentrations/index.shtml 

(last visited Nov. 16, 2010); Jassby, supra note 116; 2010 Ammonia Update Memorandum from Christopher Foe, 

Cal. Reg’l Water Quality Bd. Cent. Valley Region to Jeff Bruns & Karen Taberski , Water Boards (Oct. 7, 2010), 

available at

http://www.waterboards.ca.gov/centralvalley/water_issues/delta_water_quality/ambient_ammonia_concentrations/o

ct2010_staffupdate_ammonia.pdf.

119 ADAM BALLARD ET AL., INTERAGENCY ECOLOGICAL PROGRAM, BACKGROUND/SUMMARY OF AMMONIA 

INVESTIGATIONS IN THE SACRAMENTO-SAN JOAQUIN DELTA AND SUISUN BAY (2009), available at 

http://science.calwater.ca.gov/pdf/workshops/workshop_ammonia_bckgrnd_paper_nh4-nh3_030209.pdf; August 

2009 Ammonia Update Memorandum from Christopher Foe, Cal. Reg’l Water Quality Bd. Cent. Valley Region to 

Jeff Bruns & Sue McConnell, Water Boards (Sept. 24, 2009), available at

http://www.waterboards.ca.gov/centralvalley/water_issues/delta_water_quality/ambient_ammonia_concentrations/a

mmonia_mem.pdf; 2010 Ammonia Update Memorandum from Christopher Foe, supra note 118.

120 Glibert, supra note 49.

121 David Fullerton, Metro. Water Dist., Ammonium Concentrations and the Food Chain in Suisun Bay and the 

Delta, Presented at the Ammonia Summit at the Central Valley Regional Water Quality Control Board (Aug. 18-19, 

2009), 

http://www.swrcb.ca.gov/rwqcb5/water_issues/delta_water_quality/ambient_ammonia_concentrations/18aug09_am

monia_summit/fullerton_pres.pdf. 

122 Inge Werner et al., The Effects of Wastewater Treatment Effluent Associated Contaminants on Delta Smelt, UNIV.

OF CAL. DAVIS AQUATIC TOXICOLOGY LAB. 1, 60 (2008), available at 

http://www.water.ca.gov/pubs/environment/interagency_ecological_program/ammonia/the_effects_of_wastewater_t

reatment_effluentassociated_contaminants_on_delta_smelt.__final_report/werner_delta_smelt_ammonia_final_report012809.pdf; 

Inge Werner et al., Acute Toxicity of Ammonia/um and Wastewater Treatment Effluent-Associated Contaminants on 

Delta Smelt, UNIV. OF CAL. DAVIS AQUATIC TOXICOLOGY LAB. 1, 63 (2009), available at 

http://www.science.calwater.ca.gov/pdf/workshops/POD/UCDATL_FINAL_REPORT_Delta%20Smelt%20Ammonia_2009.pdf; CHRISTOPHER FOE, ADAM BALLARD &

STEPHANIE FONG, CENT. VALLEY REG’L WATER QUALITY CONTROL BD., NUTRIENT CONCENTRATIONS AND 

BIOLOGICAL EFFECTS IN THE SACRAMENTO-SAN JOAQUIN DELTA (July 2010).

123 Werner et al., Acute Toxicity of Ammonia/um and Wastewater Treatment Effluent-Associated Contaminants on 

Delta Smelt, supra note 122, at 63.

124 FOE, BALLARD & FONG, supra note 122.

125 S.J. Teh, Univ. of Cal. Davis, Aquatic Toxicology Program., Acute Toxicity of Ammonia, Copper, and Pesticides 

to Key Copepods, Pseudodiaptomus forbesi and Eurytemora affinis, of the San Francisco Estuary, Presented at the 

Ammonia Summit at the Central Valley Regional Water Quality Control Board (Aug. 18-19, 2009), 

http://www.swrcb.ca.gov/rwqcb5/water_issues/delta_water_quality/ambient_ammonia_concentrations/18aug09_am

monia_summit/teh_pres.pdf.

126 CENT. VALLEY REG’L WATER QUALITY CONTROL BD, TENTATIVE NPDES PERMIT FOR SACRAMENTO COUNTY 

REGIONAL SANITATION DISTRICT, REGIONAL WASTEWATER TREATMENT PLANT, ATTACHMENT K (Sept. 3, 2010).

127 Id.; Teh, supra note 125.

128 Teh, supra note 125; Randall & Tsui, supra note 109; F. B. Eddy, Ammonia in Estuaries and Effects on Fish, 67 

J. OF FISH BIOLOGY 1495, 1495-1513 (2005).

129 Jassby, supra note 107; Wilkerson et al., supra note 117.

130 Cloern, supra note 50; P.W. Lehman, The Influence of Climate on Phytoplankton Community Biomass in San 

Francisco Bay Estuary, 45 LIMNOLOGY & OCEANOGRAPHY (3) 580, 580-90 (2000).

131 Lehman, supra note 130; T. Brown, Phytoplankton Community Composition: The Rise of the Flagellates, 22IEP

NEWSLETTER (3) 20, 20-27 (2009), available at

http://www.water.ca.gov/iep/newsletters/2009/IEPNewsletter_Final2SUMMER-Fall2009%20.pdf; J. E. Cloern & R. 

Dufford, Phytoplankton Community Ecology: Principles Applied in San Francisco Bay, 258 MARINE ECOLOGY 

PROGRESS SERIES 11, 11-28 (2005). 

132 James Orsi, Food Habits of Several Abundant Zooplankton Species in the Sacramento-San Joaquin Estuary, IEP

TECHNICAL REPORT No. 41 (Feb., 1995).
72

 

133 Id.

134 Michael T. Brett & Dorthe C. Muller-Navarra, The Role of Highly Unsaturated Fatty Acids in Aquatic Foodweb 

Processes, 38 FRESHWATER BIOLOGY 483, 483-99 (1997).

135 Benni Hanson, Peter Koefoed Bjornsen & Per Juel Hansen, The Size Ratio Between Planktonic Predators and 

their Prey, 39(2) LIMNOLOGY & OCEANOGRAPHY 395, 395-403 (1994); Tom Fenchel, Marine Plankton Food 

Chains, 19 ANNUAL REVIEW OF ECOLOGY EVOLUTION & SYSTEMATICS 19, 19-38 (1988).

136 Glibert, supra note 49.

137 Gry Mine Berg et al., Variability in Inorganic and Organic Nitrogen Uptake Associated with Riverine Nutrient 

Input in the Gulf of Riga, Baltic Sea, 24 ESTUARIES 204, 204-14 (2001). 

138 Quay Dortch, The Interaction Between Ammonium and Nitrate Uptake in Phytoplankton, 61 MARINE ECOLOGY 

PROGRESS SERIES 183, 183-201(1990).

139 Dugdale, Wilkerson, Hogue & Marchi, supra note 46; Wilkerson et al., supra note 117.

140 Lehman, supra note 130; Cloern, supra note 50.

141 P.W. Lehman et al., Initial Impacts of Microcystis aeruginosa Blooms on the Aquatic Food Web in the San 

Francisco Estuary, 637 HYDROBIOLOGIA 229, 229-48 (2010).

142 P.W. Lehman, G. Boyer, C. Hall, S. Waller & K. Gehrts, Distribution and Toxicity of a New Colonial 

Microcystis aeruginosa Bloom in the San Francisco Bay Estuary, California, 541 HYDROBIOLOGIA 87, 87-99 

(2005).

143 C. E. Mioni, Does Ammonia Impact the Distribution of Harmful Algae and Phototoxins in the San Francisco 

Estuary?, Presented at the Ammonia Summit at the Central Valley Regional Water Quality Control Board (Aug. 18-

19, 2009), 

http://www.swrcb.ca.gov/rwqcb5/water_issues/delta_water_quality/ambient_ammonia_concentrations/18aug09_am

monia_summit/mioni_pres.pdf.

144 Lehman, supra note 130; Lehman et al., supra note 141; P.W. Lehman, G. Boyer, M. Satchwell & S. Waller, The 

Influence of Environmental Conditions on the Seasonal Variation of Microcystis Cell Density and Microcystins 

Concentration in the San Francisco Estuary, 600 HYDROBIOLOGIA 187, 187-204 (2008).

145 SAN FRANCISCO REG’L WATER QUALITY CONTROL BD., WATER QUALITY CONTROL PLAN (BASIN PLAN) FOR THE 

SAN FRANCISCO BAY BASIN (2006), available at

http://www.waterboards.ca.gov/sanfranciscobay/basin_planning.shtml.

146 U.S. ENVTL. PROT. AGENCY, supra note 108.

147 U.S. ENVTL. PROT. AGENCY, supra note 110.

148 Diana Engle, Larry Walker Assoc., Total Ammonia and Un-ionized Ammonia Concentrations in the Delta: An 

Examination of Ambient Concentrations and Toxicity Thresholds, Presented at the Ammonia Summit at the Central 

Valley Regional Water Quality Control Board (Aug. 18-19, 2009), 

http://www.swrcb.ca.gov/centralvalley/water_issues/delta_water_quality/ambient_ammonia_concentrations/index.s

html.

149 S Teh, supra note 125.

150 Werner et al., The Effects of Wastewater Treatment Effluent Associated Contaminants on Delta Smelt, supra note

122, at 60.

151 FOE, BALLARD & FONG, supra note 122.

152 U.S. ENVTL. PROT. AGENCY, DRAFT 2009 UPDATE AQUATIC LIFE AMBIENT WATER QUALITY CRITERIA FOR 

AMMONIA – FRESHWATER FACTSHEET (2009), available at

http://www.epa.gov/waterscience/criteria/ammonia/factsheet2.html.

153 FOE, BALLARD & FONG, supra note 122.

154 Letter from Walter Wadlow, Gen. Manager, Alameda County Water Dist. et al., to Kathleen Harder, Water Res. 

Control Eng’r, Cal. Reg’l Water Quality Control Bd., Cent. Valley Region, (June 1, 2010), available at

http://www.swrcb.ca.gov/centralvalley/board_decisions/tentative_orders/aquatictox/wateragencies_aqtox_com.pdf 

(regarding aquatic life and wildlife preservation issues concerning Sacramento Regional Wastewater Treatment 

Plant NPDES Permit Renewal).

155 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., NPDES PERMIT RENEWAL ISSUES AQUATIC LIFE AND 

WILDLIFE PRESERVATION SACRAMENTO REGIONAL COUNTY SANITATION DISTRICT SACRAMENTO REGIONAL 

WASTEWATER TREATMENT PLANT (Apr. 28, 2010), available at 

http://www.swrcb.ca.gov/centralvalley/board_decisions/tentative_orders/aquatictox/aquatictox_iss_pap.pdf.

156 Sacramento County Regional Sanitation District, Regional Wastewater Treatment Plant, NPDES Permit Order
73

 

No. R5-2010-0014 (Dec. 9, 2010), available at 

http://www.waterboards.ca.gov/centralvalley/board_decisions/adopted_orders/sacramento/r5-2010-0114_npdes.pdf.

157 Central Valley Regional Water Quality Control Board, Adopted Orders, 

http://www.swrcb.ca.gov/centralvalley/board_decisions/adopted_orders/index.shtml (last visited Dec. 3, 2010) (All 

data come from these NPDES permits)

158 Stockton NPDES Permit, Order No. R5-2002-0083 (2002).

159 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., WASTE DISCHARGE REQUIREMENTS AND NPDES PERMIT 

FOR THE CITY OF STOCKTON WASTEWATER TREATMENT CONTROL FACILITY NPDES PERMIT R5-2008-0154 (Oct. 

23, 2008), available at http://www.swrcb.ca.gov/centralvalley/board_decisions/adopted_orders/san_joaquin/r5-

2008-0154.pdf.

160 FOE, BALLARD & FONG, supra note 122.

161 The term bioaccumulation is used in this context to refer both to biomagnification (increasing concentration in a 

food web through trophic transfer) and bioaccumulation (build-up in an organism over time). 

162 A. Dennis Lemly, Environmental Implications of Excessive Selenium, 10 BIOMEDICAL & ENVTL. SCIENCES 415, 

415 (1997).

163 A. Robin Stewart et al., Food Web Pathway Determines How Selenium Affects Ecosystems: A San Francisco Bay 

Case Study, 38 ENVTL. SCI.TECH. 4519, 4519-26 (2004).

164 PETER M. CHAPMAN ET AL., ECOLOGICAL ASSESSMENT OF SELENIUM IN THE AQUATIC ENVIRONMENT 5 (2010) 

(Evidence has been mounting for several decades); See U.S. FISH & WILDLIFE SERV./ NAT’L MARINE FISHERIES 

SERV. BIOLOGICAL OPINION ON THE CALIFORNIA TOXICS RULE 123 (2000) (concluded that “[N]early every major 

review of experimental and field data conducted over the past decade has concluded that a chronic criterion of 5 

micrograms/L is not fully protective of aquatic life” and that there was an “overwhelming” weight of evidence 

supporting a concentration no greater than 2 microg./L ); California Toxics Rule, Establishment of Numeric Criteria 

for Priority Toxic Pollutants for the State of California, 40 C.F.R. § 131.38 (May 18, 2000).

165 Selenium toxicity is more a concern with wildlife and aquatic life, rather than human health. However, there are 

regulatory measures to protect humans. As with fish and wildlife, human exposure to selenium occurs through food 

and to a lesser degree, drinking water. Human health requirements (infants to adults: 15-55 micrograms/L) are 

generally met without supplements. Inadvertent human exposure to excessive amounts of selenium is unlikely, 

except through consumption of contaminated fish or meat. See PESTICIDE & ENVTL. TOXICOLOGY BRANCH, OFFICE 

OF ENVTL. HEALTH HAZARD ASSESSMENT, PUBLIC HEALTH GOAL FOR SELENIUM IN DRINKING WATER (Apr. 2010) 

(OEHHA has developed a fish contaminant goal for selenium and advisory levels for selenium in fish tissue. 

OEHHA also is responsible for issuing consumption warnings for sport or subsistence fishing sites where there is 

evidence of contaminated fish. At present, there are no consumption warnings for selenium in the Bay Delta 

Estuary watershed. The drinking water standard, or “maximum contamination level” (MCL), established by the 

California Department of Public Health for public water systems is 50 parts per billion (ppb) for selenium. This 

value may be reevaluated on the basis of recent OEHHA research on human health risk that recommends a 30 ppb 

goal).

166 Under highly anoxic conditions (for example, buried sediments) selenium can be reduced to elemental selenium, 

but selenium does not readily return to elemental form after conversion to bioavailable forms. 

167 Andrew N. Cohen, Guide to the Exotic Species of San Francisco Bay (2005), http://www.exoticsguide.org (last 

visited Nov. 4, 2010).

168 WILLIAM N. BECKON & THOMAS C. MAURER, U.S. DEP’T OF THE INTERIOR, FISH & WILDLIFE SERVICE, SPECIES 

AT RISK FROM SELENIUM EXPOSURE IN THE SAN FRANCISCO ESTUARY, 1, 51-52 (Mar. 2008) (Beckon and Maurer 

report that little is known of risk of selenium to green sturgeon).

169 WILLIAM N. BECKON & THOMAS C. MAURER, POTENTIAL EFFECTS OF SELENIUM CONTAMINATION ON 

FEDERALLY-LISTED SPECIES RESULTING FROM DELIVERY OF FEDERAL WATER TO THE SAN LUIS UNIT (Mar. 2008), 

available at

http://wwwrcamnl.wr.usgs.gov/Selenium/Library_articles/Beckon_and_Maurer_Effects_of_Se_on_Listed_Species_

SLD_2008.pdf.

170 SAN FRANCISCO ESTUARY INSTITUTE FOR THE GRASSLAND BYPASS PROJECT OVERSIGHT COMMITTEE,

GRASSLAND BYPASS PROJECT ANNUAL REPORT 2006-2007 14 (2010), available at

http://www.sfei.org/sites/default/files/GBP%20Annual%20Report%200607%20for%20web_1.pdf (Loading from 

the Grassland Bypass Project was over 8,000 lbs/year between 1986-96 (pre-project), compared with 3,300/year a 

decade into the Project (2005-07). Subsequently, loads have continued to decline, but at a slower rate); SAN 
74

 

FRANCISCO BAY REG’L WATER QUALITY CONTROL BD., TECHNICAL MEMORANDUM 2: NORTH BAY SELENIUM 

DATA SUMMARY AND SOURCE ANALYSIS 3-29 (July 2008), available at 

http://www.swrcb.ca.gov/rwqcb2/water_issues/programs/TMDLs/northsfbayselenium/TMDL_TM2_July2008.pdf 

(The refinery discharges have also shifted from selenite to selenate (the less bioavailable form)).

171 Id.

172 National Toxics Rule, 40 C.F.R. § 131.36 (Dec. 22, 1992); California Toxics Rule, Establishment of Numeric 

Criteria for Priority Toxic Pollutants for the State of California, 40 C.F.R. § 131.38 (May 18, 2000) (On May 18, 

2000, the EPA promulgated numeric water quality criteria for priority toxic pollutants and other provisions for water 

quality standards to be applied to waters in the State of California. The rule filled a gap in California water quality 

standards that was created in 1994 when a state court overturned the state's water quality control plans containing 

water quality criteria for priority toxic pollutants. The criteria became legally applicable in the State of California 

for inland surface waters, enclosed bays and estuaries for all purposes and programs under the Clean Water Act).

173 California Toxics Rule, 40 C.F.R. § 131.38 (May 18, 2000); National Toxics Rule, 40 C.F.R. § 131.36 (Dec. 22, 

1992).

174 See CENT. VALLEY REG’L WATER QUALITY CONTROL BD., STAFF REPORT: TMDL FOR SELENIUM IN THE LOWER 

SAN JOAQUIN RIVER 1, 2-3 (Aug. 2001) (In 1996 the Central Valley RWQCB adopted the 5 micrograms/L chronic 

value, incorporating it into the Basin Plan. This objective still applies to Mud Slough and the San Joaquin River 

from Sack Dam to Vernalis. This action also set a 2 micrograms/L chronic value for the Grasslands channels and 

Salt Slough); See CENT. VALLEY REG’L WATER QUALITY CONTROL BD., 1996 BASIN PLAN AMENDMENT (1996), 

available at

http://www.swrcb.ca.gov/rwqcb5/water_issues/water_quality_studies/surface_water_ambient_monitoring/historic_r

eports_and_faq_sheets/index.shtml#1996bpa (The site-specific objectives adopted by the Regional Board for the 

Grasslands Marshes and Salt Slough were based in part on consideration of the lentic conditions, but this approach 

has not been applied consistently throughout the watershed). 

175 U.S. FISH & WILDLIFE SERV., supra note 164(The Services found that "the chronic aquatic life criterion for 

selenium proposed in the CTR does not protect listed fish and wildlife dependent on the aquatic ecosystem for 

development and/or foraging").

176 THERESA S. PRESSER & SAMUEL N. LUOMA, FORECASTING SELENIUM DISCHARGES TO THE SAN FRANCISCO BAYDELTA ESTUARY, U.S. GEOLOGICAL SURVEY PROFESSIONAL PAPER 1646, 55, 55-63 (2006), available at 

http://pubs.usgs.gov/pp/p1646.

177 Theresa Presser & Samuel N. Luoma, A Methodology for Ecosystem-Scale Modeling of Selenium, 6 INTEGRATED 

ENVTL. ASSESSMENT & MGMT. 685, 685-710 (2010), available at 

http://onlinelibrary.wiley.com/doi/10.1002/ieam.101/abstract.

178 AMY E. KLECKNER ET AL., U.S. GEOLOGICAL SURVEY OPEN-FILE REPORT 2010-1252, SELENIUM 

CONCENTRATIONS AND STABLE ISOTOPIC COMPOSITIONS OF CARBON AND NITROGEN IN THE BENTHIC CLAM 

CORBULA AMURENSIS FROM NORTHERN SAN FRANCISCO BAY, CALIFORNIA: MAY 1995-FEBRUARY 2010 (2010), 

available at http://pubs.usgs.gov/of/2010/1252/.

179 Presser & Luoma, supra note 177 at 685-710 (This work is pursuant to two agreements reached following an 

ESA consultation and Biological Opinion on the California Toxics Rule; U.S. EPA agreed to develop and 

promulgate as part of the California Toxics Rule aquatic life criteria for listed species).

180 STATE WATER RES. CONTROL BD., supra note 94.

181 STATE WATER RES. CONTROL BD., WATER QUALITY CONTROL POLICY FOR DEVELOPING CALIFORNIA’S CLEAN 

WATER ACT SECTION 303(D) LIST (Sept. 2004), available at 

http://www.swrcb.ca.gov/water_issues/programs/tmdl/docs/ffed_303d_listingpolicy093004.pdf.

182 STATE WATER RES. CONTROL BD., supra note 94; See Letter from Alexis Strauss, supra note 94.

183 The permits are: Chevron Products Company, Richmond Refinery, CA0005134 (expires 6/13/2011); 

ConocoPhillips, San Francisco Refinery, CA0005053 (expires 6/15/2011); Shell Oil U.S. and Equilon Enterprises 

LLC, Shell Martinez Refinery, CA0005789 (expires 10/31/2011); Tesoro Refining and Marketing Co., Golden 

Eagle Refinery, CA0004961 (expires 6/30/2015); and Valero Refining Company, CA, Valero Benicia Refinery, 

CA0005550 (expires 11/31/2014).

184 SAN FRANCISCO BAY REG’L WATER QUALITY CONTROL BD., supra note 170, at 3-61.

185 San Francisco Bay Regional Water Quality Control Board, Amendment of Waste Discharge Requirements for 

San Francisco Bay Region Refineries, Order No. R2-2010-0057 (2010).

186 U.S. BUREAU OF RECLAMATION, SAN LUIS UNIT DRAINAGE FEATURE RE-EVALUATION, FINAL ENVIRONMENTAL 
75

 

IMPACT STATEMENT & RECORD OF DECISION 7 (Mar. 2007).

187 In this area a strict distinction between surface and groundwater, or focus only on surface water, is misplaced. 

Water management in the Basin mixes both sources. Also, there is evidence that subsurface flow from areas that do 

not discharge to surface waters may affect the shallow groundwater in areas near the San Joaquin River, where 

surface-groundwater interchange is active.

188 U.S. EPA List of Approved Selenium TMDLs, 

http://oaspub.epa.gov/tmdl/waters_list.tmdls?region=9&polid=20&pollutant=SELENIUM (last visited Nov. 4, 

2010) (includes TMDLs for Selenium in the Lower San Joaquin River (2002), Grasslands Marshes (2000), and Salt 

Slough (1999)); See also Central Valley Regional Water Quality Control Board, San Joaquin River Selenium 

TMDL, http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/central_valley_projects/san_joaquin_se/index.shtml 

(last visited Nov. 4, 2010).

189 In the future, this current framework may be augmented by, or coordinated more closely with, related programs. 

One example is tracking with the Irrigated Lands Regulatory Program, which has recently proposed significant 

changes in program scope and approach, including covering discharges to groundwater. The Grasslands Bypass 

Project area has not been required to participate directly in the ILRP because the Grasslands Bypass Project is 

considered generally equivalent to the ILRP requirements. Closer ties are also anticipated between the Grasslands 

Bypass Project and the Long Term Sustainability Initiative (CV-SALTS) to develop a comprehensive regional salt 

management plan. 

190 The Use Agreement sets out an incentive fee structure to promote compliance with target load reductions and 

defines multi-agency oversight (in which EPA participates) and technical groups. The Grasslands Bypass Project 

also has a relatively comprehensive surface water monitoring program with results posted at http://www.sfei.org/gbp 

(last visited Nov. 16, 2010).

191 SAN FRANCISCO ESTUARY INSTITUTE FOR THE GRASSLAND BYPASS PROJECT OVERSIGHT COMMITTEE, supra note 

170 (To some extent, the drainers can avoid discharges of selenium to surface waters by storing or placing it 

elsewhere—notably in shallow groundwater of reuse areas and in uses such as road wetting (termed ‘displacement’ 

in the Grasslands Report). Reduction in drainage volume in reuse areas facilitates use of this ‘storage’ in lieu of 

surface discharges, but can concentrate selenium). 

192 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., AMENDMENTS TO THE WATER QUALITY CONTROL PLAN 

FOR THE SACRAMENTO RIVER AND SAN JOAQUIN RIVER BASINS TO ADDRESS SELENIUM CONTROL IN THE SAN 

JOAQUIN RIVER BASIN FINAL STAFF REPORT 6 (May 2010).

193 In May 2010, the Central Valley Regional Water Quality Control Board gave its approval for extended time 

through a Basin Plan Amendment; the State Board approved it on October 5, 2010. The action will be followed by 

revised waste discharge requirements. 

194 PRESSER & LUOMA, supra note 176 at 20 (This selenium reservoir is such that increased applied irrigation water 

does not dilute selenium concentration; rather, concentration increases).

195 Analysis of San Joaquin Basin selenium has a long history. See U.S. DEP’T OF THE INTERIOR & CAL. RES.

AGENCY, A MANAGEMENT PLAN FOR AGRICULTURAL SUBSURFACE DRAINAGE AND RELATED PROBLEMS ON THE 

WESTSIDE SAN JOAQUIN VALLEY (Sept. 1990); U.S. BUREAU OF RECLAMATION, supra note 186; San Joaquin Valley 

Drainage Documents, http://www.archive.org/search.php?query=San%20Joaquin%20Valley%20Drainage (last 

visited Oct. 21, 2010); Kesterson Reservoir Documents, http://www.archive.org/search.php?query=kesterson (last 

visited Oct. 21, 2010). 

196 U.S. EPA, About Pesticides, www.epa.gov/pesticides/about/index.htm (last visited Oct. 21, 2010).

197 U.S. GEOLOGICAL SURVEY, PESTICIDES IN SURFACE AND GROUND WATER OF THE UNITED STATES: SUMMARY OF 

THE RESULTS OF THE NATIONAL WATER QUALITY ASSESSMENT PROGRAM (NAWQA) (2006), available at 

http:/pubs.usgs.gov/circ/2005/1291.

198 STATE WATER RES. CONTROL BD., supra note 94.

199 CHRISTOPHER FOE & VALERIE CONNOR, STAFF REPORT CENT. VALLEY REG’L WATER QUALITY CONTROL BD.,

1989 RICE SEASON TOXICITY MONITORING RESULTS (1991), available at

http://www.calwater.ca.gov/Admin_Record/C-029766.pdf.

200 CHRISTOPHER FOE & VALERIE CONNOR, STAFF REPORT CENT. VALLEY REG’L WATER QUALITY CONTROL BD.,

SAN JOAQUIN WATERSHED BIOASSAY RESULTS, 1988-1990 (1991).

201 Kathryn Kuivila & Christopher Foe, Concentrations, Transport and Biological Effects of Dormant Spray 

Pesticides in the San Francisco Estuary, California, 14 ENVTL. TOXICOLOGY & CHEMISTRY 1141, 1141-50 (1995).

202 Howard C. Bailey et al., Diazinon and Chlorpyrifos in Urban Waterways in Northern California, USA, 19 
76

 

ENVTL. TOXICOLOGY & CHEMISTRY 82, 82-87 (2000); VALERIE CONNOR, STAFF MEMORANDUM STATUS OF URBAN 

STORM RUNOFF PRODUCTS, ALGAL TOXICITY AND HERBICIDE LEVELS ASSOCIATED WITH URBAN STORM RUNOFF,

DIAZINON AND CHLORPYRIFOS DETECTIONS IN THE SAN FRANCISCO BAY AREA, as reported in CHRISTOPHER FOE,

STAFF REPORT CENT. VALLEY REG’L WATER QUALITY CONTROL BD., EVALUATION OF THE POTENTIAL IMPACT OF 

CONTAMINANTS ON AQUATIC RESOURCES IN THE CENTRAL VALLEY AND SACRAMENTO-SAN JOAQUIN DELTA 

ESTUARY (1995).

203 CHRISTOPHER FOE, LINDA DEANOVIC & DAVE HINTON, STAFF REPORT CENT. VALLEY REG’L WATER QUALITY 

CONTROL BD. TOXICITY IDENTIFICATION EVALUATIONS OF ORCHARD DORMANT SPRAY RUNOFF (1998).

204 CHRISTOPHER FOE & R. SHEIPLINE, STAFF REPORT CENT. VALLEY REG’L WATER QUALITY CONTROL BD.,

PESTICIDES IN SURFACE WATER FROM APPLICATIONS ON ORCHARDS AND ALFALFA DURING THE WINTER AND 

SPRING OF 1991-1992 (1993).

205 Donald Weston & Michael J. Lydy, Pyrethroid Insecticides to the Sacramento-San Joaquin Delta of California, 

44 ENVTL. SCI. & TECH. 1833, 1833-40 (2010).

206 STATE WATER RES. CONTROL BD., supra note 94.

207 Id.

208 “Unknown toxicity” is an impairment category that documents toxic events (widespread aquatic organism 

mortality in one location) that results from unidentified contaminants and their unidentified sources. 

209 FOE & CONNOR, supra note 200; FOE & SHEIPLINE, supra note 204; Weston & Lydy, supra note 205.

210 URBAN PESTICIDE POLLUTION PREVENTION PROJECT, PESTICIDES OF INTEREST FOR URBAN SURFACE WATER 

QUALITY, URBAN PESTICIDES USE TRENDS ANNUAL REPORT (2008), available at

http://www.up3project.org/documents/UP3UseTrendsReport2008.pdf.

211 Including the Sacramento and San Joaquin River Basins, Bay Delta Estuary, and San Francisco Bay watersheds.

212 Reported for pesticides applied in amounts greater than 500 kg (0.5 tons or ~1100 pounds).

213 Kathryn Kuivila & Michelle Hladik, Understanding the Occurrence and Transport of Current-Use Pesticides in 

the San Francisco Estuary Watershed, 6(3) SAN FRANCISCO ESTUARY & WATERSHED SCI. 1, 1-19 (2008).

214 URBAN PESTICIDE POLLUTION PREVENTION PROJECT, supra note 210.

215 JOHNSON, supra note 104; Nathaniel Schloz, Pesticides and the Decline of Pelagic Fishes in Western North 

America’s Largest Estuarine Ecosystem CONSERVATION LETTERS (forthcoming 2011); NATIONAL RESEARCH 

COUNCIL, COMMITTEE ON SUSTAINABLE WATER AND ENVIRONMENTAL MANAGEMENT IN THE CALIFORNIA BAYDELTA, A SCIENTIFIC ASSESSMENT OF ALTERNATIVES FOR REDUCING WATER MANAGEMENT EFFECTS ON 

THREATENED AND ENDANGERED FISHES IN CALIFORNIA’S BAY DELTA (2010), available at

http://www.nap.edu/catalog.php?record_id=12881.

216 Kuivila & Moon, supra note 44.

217 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., WATER QUALITY CONTROL PLAN FOR THE SACRAMENTO 

AND SAN JOAQUIN RIVER BASINS (2009), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/basin_plans/index.shtml.

218 Inge Werner et al., Insecticide-Caused Toxicity to Ceriodaphnia dubia (Cladocera) in the Sacramento–San 

Joaquin River Delta, California, USA, 19 ENVTL. TOXICOLOGY & CHEMISTRY 215, 215-27 (2000); Kuivila & Moon, 

supra note 44.

219 Kuivila & Moon, supra note 44.

220 Bennett, supra note 38.

221 David Ostrach et al., Maternal Transfer of Xenobiotics and Effects on Larval Striped Bass in the San Francisco 

Estuary,105 PROCEEDINGS OF THE NAT’L ACAD. OF SCI. 19354, 19354-59 (2008). 

222 DANIEL OROS & INGE WERNER, WHITE PAPER FOR THE INTERAGENCY ECOLOGICAL PROGRAM, SFEI

CONTRIBUTION 415, PYRETHROID INSECTICIDES: AN ANALYSIS OF USE PATTERNS, DISTRIBUTIONS, POTENTIAL 

TOXICITY AND FATE IN THE SACRAMENTO-SAN JOAQUIN DELTA AND CENTRAL VALLEY (2005), available at 

http://www.science.calwater.ca.gov/pdf/workshops/POD/CDFG_POD_Pyrethroids_White_Paper_Final_PDF.pdf.

223 PETER MOYLE, INLAND FISHES OF CALIFORNIA 405 (1976) as reported in OROS & WERNER, supra note 222.

224 S. OBREBSKI, J.J. ORSI & W. KIMMERER, IEP TECHNICAL REPORT NO. 32, LONG TERM TRENDS IN ZOOPLANKTON 

DISTRIBUTION AND ABUNDANCE IN THE SACRAMENTO-SAN JOAQUIN ESTUARY (1992).

225 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., DELTA DIAZINON AND CHLORPYRIFOS TMDL-FINAL 

BASIN PLAN AMENDMENT STAFF REPORT (June 2006), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/delta_op_pesticide/final_staff_rep

ort/index.shtml; OROS & WERNER, supra note 222.
77

 

226 STATE WATER RES. CONTROL BD., supra note 94.

227 URBAN PESTICIDE POLLUTION PREVENTION PROJECT, supra note 210.

228 OROS & WERNER, supra note 222.

229 Kuivila & Hladik, supra note 213.

230 Bailey et al., supra note 202; Howard Bailey et al., Joint Acute Toxicity of Diazinon and Chlorpyrifos to 

Ceriodaphnia dubia, 16 ENVTL. TOXICOLOGY & CHEMISTRY 2304, 2304-08 (1997); Michael Lydy & K. R. Austin, 

Toxicity Assessment of Pesticide Mixtures Typical of the Sacramento–San Joaquin Delta using Chironomus tentans, 

48 ARCHIVES OF ENVTL. CONTAMINATION & TOXICOLOGY 49, 49–55 (2004).

231 M. Faust et al., Additive Effects of Herbicide Combinations on Aquatic Non-Target Organisms, 134 SCI. OF THE 

TOTAL ENV’T (Supplement 2) 941, 941-52 (1993).

232 Teresa Norberg-King et al., Application of Toxicity Identification Evaluation Procedures to the Ambient Waters 

of the Colusa Basin Drain, California, 10 ENVTL. TOXICOLOGY & CHEMISTRY 891, 891-900 (1991).

233 Debra Denton et al., Joint Acute Toxicity of Esfenvalerate and Diazinon to Larval Fathead Minnows (Pimephales 

promelas), 22 ENVTL. TOXICOLOGY & CHEMISTRY 336, 336-41 (2003).

234 Lydy & Austin, supra note 230.

235 OROS & WERNER, supra note 222.

236 URBAN PESTICIDE POLLUTION PREVENTION PROJECT, supra note 210.

237 Kuivila & Hladik, supra note 213.

238 ZHIMIN LU & GENE DAVIS, CENT. VALLEY REG’L WATER QUALITY CONTROL BD. STAFF REPORT, RELATIVERISK EVALUATION FOR PESTICIDES USED IN THE CENTRAL VALLEY PESTICIDES BASIN PLAN AMENDMENT PROJECT 

AREA (2010), available at

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/central_valley_pesticides/risk_eva

luation/rre_stff_rpt_feb2009_final.pdf.

239 Weston & Lydy, supra note 205; Ostrach et al., supra note 221.

240 Schloz, supra note 215; Michael J. Lydy et al., Challenges in Regulating Pesticide Mixtures, 9 ECOLOGY &

SOC’Y (6) 1, 1-15 (2004), available at http://www.ecologyandsociety.org/vol9/iss6/art1. 

241 Wash. Toxics Coal. v. E.P.A., No. C-01-0132C (W.D. Wash. Jan. 22, 2004).

242 National Marine Fisheries Services, Pesticide Consultations with U.S. EPA, 

http://www.nmfs.noaa.gov/pr/consultation/pesticides.htm (last visited Dec. 21, 2010) (Contains links to three NMFS 

biological opinions spanning from 2008-2010 on 18 active ingredients, as well as consultation correspondence.

These cases and consultations are very active, with related court filings and agency exchanges occurring regularly. 

The next two sets of NMFS biological opinions (on carbaryl, carbofuran and methormyl (2008), and on azinphos 

methyl, bensulide, dimethoate, disulfoton, ethoprop,fenamiphos, laled, mathamidophos, methyl parathion, phorate 

and phosmet (2010) have also been issued); U.S. EPA, Pesticides: Endangered Species Protection Program, 

http://www.epa.gov/espp/ (last visited Jan. 7, 2011) (An updated status of the litigation, consultations, and current 

pesticide restrictions, along with links to the relevant administrative and court documents).

243 U.S. EPA, supra note 242 (use restrictions and other documents associated with this consultation process).

244 These cases and consultations are very active, with related court filings and agency exchanges occurring 

regularly. An updated status of the litigation, consultations, and current pesticide restrictions, along with links to the 

relevant administrative and court documents, is available at http://www.epa.gov/espp/.

245 Ctr. for Biological Diversity v. EPA, No. 07-2794-JCS (N.D. Cal. May 17, 2010) (stipulated injunction), 

available at http://www.epa.gov/espp/litstatus/stipulated-injuc.html.

246 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., supra note 217.

247 SAN FRANCISCO REG’L WATER QUALITY CONTROL BD., SAN FRANCISCO BAY BASIN WATER QUALITY CONTROL 

PLAN (2007), available at 

http://www.swrcb.ca.gov/sanfranciscobay/water_issues/programs/basin_plan/docs/basin_plan07.pdf. 

248 STATE WATER RES. CONTROL BD., supra note 61.

249 STATE WATER RES. CONTROL BD., DRAFT POLICY FOR TOXICITY ASSESSMENT AND CONTROL (2010), available 

at http://www.waterboards.ca.gov/water_issues/programs/state_implementation_policy/docs/tox_policy.pdf.

250 STATE WATER RES. CONTROL BD., DRAFT STAFF REPORT POLICY FOR TOXICITY ASSESSMENT AND CONTROL

(2010), available at

http://www.waterboards.ca.gov/water_issues/programs/state_implementation_policy/docs/stff_rpt_tox_policy.pdf.

251 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., supra note 217.

252 Id.
78

 

253 Id.

254 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., SACRAMENTO AND SAN JOAQUIN RIVER WATERSHEDS 

PESTICIDE BASIN PLAN AMENDMENT FACT SHEET (2006), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/central_valley_pesticides/att2_fact

.pdf.

255 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., RELATIVE-RISK EVALUATION FOR PESTICIDES USED IN 

THE CENTRAL VALLEY PESTICIDE BASIN PLAN AMENDMENT PROJECT AREA (Feb. 2009), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/central_valley_pesticides/risk_eva

luation/rre_stff_rpt_feb2009_final.pdf.

256 Central Valley Regional Water Quality Control Board, Central Valley Pesticide TMDL and Basin Plan 

Amendment - Water Quality Criteria Method Development,

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/central_valley_pesticides/criteria_

method/index.shtml (last visited Nov. 4, 2010).

257 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., CENTRAL VALLEY PESTICIDE TMDL AND BASIN PLAN 

AMENDMENT - JULY 2010 PROJECT STATUS UPDATE (2010), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/central_valley_pesticides/pest_bp

a_status_jul2010.pdf.

258 STATE WATER RES. CONTROL BD., supra note 94.

259 Letter from Fred Kizito, Envtl. Sci., Cent. Valley Reg’l Water Quality Control Bd., to interested parties (May 11, 

2009) (Supplemental Information to the Notice of Public Workshop/CEQA Scoping Meeting for a Proposed Basin 

Plan Amendment to Address OC Pesticides in Several Central Valley Waterbodies), available at

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/central_valley_organochlorine_pe

sticide/2009jul07_ceqa_scoping_mtg/oc_ceqa_supscoping.pdf.

260 Central Valley Regional Water Quality Control Board, Conditional Waivers of Waste Discharge Requirements 

for Discharges from Irrigated Lands within the Central Valley Region, Resolution No. R5-2005-107 (2005), 

available at http://www.swrcb.ca.gov/centralvalley/board_decisions/adopted_orders/waivers/r5-2005-0107.pdf.

261 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., DRAFT ENVIRONMENTAL IMPACT REPORT IRRIGATED 

LANDS REGULATORY PROGRAM (2010), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/irrigated_lands/long_term_program_development/draft_progra

m_eir_july2010/peir_exec_summ.pdf.

262 Central Valley Regional Water Quality Control Board, Coalition Group Conditional Waiver of Waste Discharge 

Requirements for Discharges from Irrigated Lands, Order No. R5-2006-0053 (2006), available at 

http://www.swrcb.ca.gov/centralvalley/board_decisions/adopted_orders/waivers/r5-2006-0053_24apr08_amend.pdf.

263 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., DRAFT ENVIRONMENTAL IMPACT STATEMENT IRRIGATED 

LANDS REGULATORY PROGRAM (2010), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/irrigated_lands/long_term_program_development/draft_progra

m_eir_july2010/index.shtml.

264 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., LONG TERM ILRP DEVELOPMENT SUMMARY (Sept. 2010), 

available at

http://www.swrcb.ca.gov/centralvalley/water_issues/irrigated_lands/long_term_program_development/sept2010_pu

b_wkshps/ilrp_handout.pdf. 

265 Weston & Lydy, supra note 205.

266 The existing MS4 permits potentially affecting the Bay Delta Estuary, along with their respective service areas 

and expiration (if any) are: (1) East Contra Costa County MS4 Permit, Order No. 5-00-120 (Sept. 22, 2010) (City of 

Antioch, City of Brentwood, City of Oakley, Contra Costa County, and Contra Costa County Flood Control and 

Water Conservation District); (2) Sacramento County MS4 Permit, Order No. R5-2008-0142 (2008) (County of 

Sacramento and Cities of Citrus Heights, Elk Grove, Folsom, Galt, and Sacramento Stormwater Discharges From 

Municipal Separate Storm Sewer Systems); (3) City of Stockton/San Joaquin County MS4 Permit (City of Stockton 

and County of San Joaquin Storm Water Discharges from Municipal Separate Storm Sewer System); (4) Port of 

Stockton MS4 Permit, Order No. R5-2004-0136 (Expired Oct. 2009) (Stockton Port District); (5) City of Modesto 

MS4 Permit (City of Modesto); and (6) Fresno MS4 Permit, Order No. 5-00-148 (Expired Mar. 2006) (Fresno 

County, Fresno Metropolitan Flood Control District, City of Fresno, City of Clovis, and California State University 

of Fresno). In addition, the State Water Resources Control Board adopted a General Permit for the Discharge of 

Storm Water from Small MS4s (WQ Order No. 2003-0005-DWQ (2003)) to provide permit coverage for smaller 
79

 

municipalities, including non-traditional Small MS4s, which are governmental facilities such as military bases, 

public campuses, and prison and hospital complexes.

267 California Construction General Permit, Water Quality Order No. 2009-0009-DWQ (2009).

268 40 C.F.R. § 450.21(d)(2) (Feb. 1, 2010) (emphasis added). 

269 See 40 C.F.R. §§ 122.43-44 (Apr. 11, 2007).

270 California Industrial Stormwater General Permit, Water Quality Order No. 97-03-DWQ (1997).

271 See 40 C.F.R. § 122.35 (Dec. 8, 1999); 40 C.F.R. § 122.26(a)(9)(i)(C)-(D) (June 12, 2006).

272 For example, the Lahontan Regional Water Quality Control Board designated all jurisdictional areas of the City 

of South Lake Tahoe, El Dorado County, and Placer County that fall within the Lake Tahoe Hydrologic Unit as 

Phase I MS4, even though this area does not meet the population threshold requirements of a Phase I MS4.

273 U.S. ENVTL. PROT. AGENCY, DRAFT GENERAL PERMIT FOR RESIDUALLY DESIGNATED DISCHARGES IN MILFORD,

BELLINGHAM, AND FRANKLIN, MASSACHUSETTS (2010), available at 

http://www.epa.gov/region1/npdes/charlesriver/index.html (last visited Nov. 4, 2010)(emphasis added).

274 See Chesapeake Bay Executive Order, Restoring and Protecting a Natural Treasure, Reports & Documents,

http://executiveorder.chesapeakebay.net/category/Reports-Documents.aspx (last visited Oct. 27, 2010). 

275 See U.S. EPA, Proposed National Rulemaking to Strengthen the Stormwater Program,

http://cfpub.epa.gov/npdes/stormwater/rulemaking.cfm (last visited Oct.27, 2010).

276 Headwaters, Inc. v. Talent Irrigation Dist., 243 F.3rd 526 (9th Cir. 2001).

277 Water Quality Order No. 2004-0008-DWQ (2004).

278 Water Quality Order No. 2004-0009-DWQ (2004). In 2006, EPA promulgated a final rule (Pesticides Rule) that 

exempted FIFRA-compliant pesticide application from needing an NPDES permit for: (1) the application of 

pesticides directly to water to control pests; and (2) the application of pesticides to control pests that are present over 

or near water, where a portion of the pesticides will unavoidably be deposited to the water to target the pests. See

71 Fed. Reg. 68,483 (Nov. 27, 2006). On January 9, 2009 the Sixth Circuit Court of Appeals, in National Cotton 

Council of America v. EPA, 553 F.3d 927 (6th Cir. 2009)(National Cotton), vacated EPA’s 2006 Pesticides Rule 

holding that the Clean Water Act unambiguously includes “biological pesticides” and “chemical pesticides” with 

residuals within its definition of “pollutant.” The Sixth Circuit granted a two-year stay of its mandate; however, by 

April 2011, NPDES permits will be required nationwide for discharges of pesticides to waters of the U.S. In 

response to the National Cotton decision, EPA has proposed a Pesticides General Permit (PGP) to cover discharges 

of pesticides to waters of the U.S. See 75 Fed. Reg. 31,775 (June 4, 2010). While the National Cotton decision 

applies nationally, the PGP will not apply in California since EPA is not the NPDES permitting authority for the 

State of California.

279 STATE WATER RES. CONTROL BD., NOTICE OF OPPORTUNITY TO PROVIDE INFORMAL COMMENTS ON 

PRELIMINARY DRAFT ADULTICIDES PERMIT (Nov. 16, 2009), available at 

http://www.swrcb.ca.gov/water_issues/programs/npdes/docs/adulticides/111609notice4comment.pdf.

280 P.J.M. Rejinders & S.M.J.M. Brasseur, Xenobiotic Induced Hormonal and Associated Development Disorders in 

Marine Organisms and Related Effects in Human; an Overview, in CHEMICALLY INDUCED ALTERATIONS IN SEXUAL 

AND FUNCTIONAL DEVELOPMENT: THE WILDLIFE/HUMAN CONNECTION 159, 159-74 (T. Colborn & C. Clement eds., 

1992).

281 C.E. Purdom et al., Estrogenic Effects of Effluents from Sewage Treatment Works, 8 CHEM. ECOLOGY 275, 275-

85 (1994); Susan Jobling et al., A Variety of Environmentally Persistent Chemicals, including some Phthalate 

Plasticizers, are Weakly Estrogenic, 103 ENVTL. HEALTH PERSPECTIVES 582, 582-87 (1995).

282 Susan Klosterhaus, San Francisco Estuary Inst., Update on Contaminants of Emerging Concern, Presentation at 

RMP Annual Meeting (Oct. 5, 2010), available at www.sfei.org/rmp/2010-Annual-Meeting.

283 M. SCHAEFER & M.L. JOHNSON, UC DAVIS AQUATIC ECOSYSTEMS ANALYSIS LABORATORY, PHARMACEUTICAL 

AND PERSONAL CARE PRODUCTS IN SURFACE WATER – OCCURRENCE, FATE AND TRANSPORT, AND EFFECT ON 

AQUATIC ORGANISMS (Oct. 2009).

284 R. Lavado et al., Site-Specific Profiles of Estrogenic Activity in Agricultural Areas of California’s Inland Waters, 

43 ENVTL. SCI. & TECH. 9110, 9110-16 (2009).

285 D.G. Joakim Larsson & L. Förlin, Male-Biased Sex Ratios of Fish Embryos Near a Pulp Mill: Temporary 

Recovery after a Short-Term Shutdown, 110 ENVTL. HEALTH PERSPECTIVES 739, 739-42 (2002); Susan Jobling et 

al., Predicted Exposures to Steroid Estrogens in U.K. Rivers Correlate with Widespread Sexual Disruption in Wild 

Fish Populations, 114 ENVTL. HEALTH PERSPECTIVES (Supplement 1) 32, 32-39 (2006).

286 Ted Sommer, Cal. Dep’t of Water Res., An Introduction to the Pelagic Organism Decline, Presentation at the 5th
80

 

Biennial CALFED Science Conference (Oct. 22-24, 2008).

287 BENNETT, HOBBS & TEH, supra note 42.

288 Id.

289 U.S. EPA, Strategy for Addressing Pharmaceuticals and Personal Care Products in Water, 

http://water.epa.gov/scitech/swguidance/ppcp/basic.cfm (last visited Nov. 4, 2010)

290 U.S. EPA, Pharmaceuticals and Personal Care Products as Pollutants,

http://www.epa.gov/ppcp/ (last visited Dec. 3, 2010) (EPA is also working to better understand and evaluate 

potential risks to human health of CECs in drinking water. This is not within the scope of this ANPR).

291 U.S. ENVTL. PROT. AGENCY, GUIDELINES FOR DERIVING NUMERICAL NATIONAL WATER QUALITY CRITERIA FOR 

THE PROTECTION OF AQUATIC ORGANISM AND THEIR USES (1985), available at

http://water.epa.gov/scitech/swguidance/waterquality/standards/current/upload/2009_01_13_criteria_85guidelines.p

df.

292 U.S. ENVTL. PROT. AGENCY, OW/ORD EMERGING CONTAMINANTS WORKGROUP, AQUATIC LIFE CRITERIA FOR 

CONTAMINANTS OF EMERGING CONCERN: GENERAL CHALLENGES AND RECOMMENDATIONS (June 3, 2008).

293 Letter from EPA’s Science Advisory Board to EPA (Dec. 18, 2008) (Review of EPA White Paper on Aquatic 

Life Criteria for Contaminants of Emerging Concern).

294 U.S. EPA, Analytical Methods: Contaminants of Emerging Concern, Pharmaceuticals and Personal Care 

Products (PPCPs) Methods Development,

http://water.epa.gov/scitech/swguidance/methods/ppcp/index.cfm (last visited Dec. 6, 2010).

295 CAL. OCEAN PROT. COUNCIL, CAL. OCEAN SCI. TRUST, NWRI, SAN FRANCISCO ESTUARY INST., S. CAL.

COASTAL WATER RES. PROJECT & URBAN WATER RES. CTR. AT THE UNIV. OF CAL., IRVINE, MANAGING 

CONTAMINANTS OF EMERGING CONCERN IN CALIFORNIA: DEVELOPING PROCESSES FOR PRIORITIZING, MONITORING,

AND DETERMINING THRESHOLDS OF CONCERN (Sept. 2009), available at http://www.sfei.org/node/2838 (based on a 

workshop held on April 28-29, 2009, in Costa Mesa, California.

296 State Water Resources Control Board, Recycled Water – Constituents of Emerging Concern,

http://www.waterboards.ca.gov/water_issues/programs/water_recycling_policy/recycledwater_cec.shtml (last 

visited Dec. 3, 2010).

297 STATE WATER RES. CONTROL BD., MONITORING STRATEGIES FOR CHEMICALS OF EMERGING CONCERN (CECS) IN 

RECYCLED WATER – RECOMMENDATIONS OF A SCIENTIFIC ADVISORY PANEL (June 25, 2010), available at

http://www.waterboards.ca.gov/water_issues/programs/water_recycling_policy/docs/cec_monitoring_rpt.pdf.

298 STATE WATER RES. CONTROL BD., CONSTITUENTS OF EMERGING CONCERN (CEC) MONITORING FOR RECYCLED 

WATER, STAFF REPORT (Nov. 8, 2010), available at

http://www.waterboards.ca.gov/water_issues/programs/water_recycling_policy/docs/cec111610/staffreport.pdf 

(presenting the recommendations for monitoring CECs in municipal recycled water).

299 Southern California Coastal Water Research Project, Project: Advisory Panel for CECs in Coastal and Marine 

Ecosystems, 

http://www.sccwrp.org/ResearchAreas/Contaminants/ContaminantsOfEmergingConcern/EcosystemsAdvisoryPanel.

aspx (last visited Dec. 3, 2010).

300 Cloern et al., supra note 40.

301 Alan D. Jassby et al., Isohaline Position as a Habitat Indicator for Estuarine Populations, 5 ECOLOGICAL 

APPLICATIONS 272, 272-89 (1995); SAN FRANCISCO ESTUARY PROJECT, MANAGING FRESHWATER DISCHARGE TO 

THE SAN FRANCISCO BAY/SACRAMENTO SAN JOAQUIN DELTA ESTUARY: THE SCIENTIFIC BASIS FOR AN ESTUARINE 

STANDARD, 127 (1993); PRINCIPLES FOR AGREEMENT ON BAY-DELTA STANDARDS BETWEEN THE STATE OF 

CALIFORNIA AND THE FEDERAL GOVERNMENT (Dec. 12, 1994) (Bay Delta Accord) (The X2 standard evolved out of 

a series of facilitated workshops involving agency and academic biologists in 1991. These workshops concluded 

that changes in the salinity gradient were strongly associated with both the distribution of most species in the San 

Francisco Bay and with the abundance of many species of the upper estuary. As an index of the Estuary’s salinity 

gradient, the workshop used the location of the low salinity zone, where average daily salinity at the bottom was 2 

ppt. This index of the salinity gradient was stated in terms of the distance in kilometers from the Golden Gate to the 

low salinity zone. The workshop coined the term X2 to represent this index. In times of high outflow, the low 

salinity zone is downstream and X2 is a smaller number. When outflow is reduced, the low salinity zone is further 

upstream and X2 is a higher number. The group recommended the use of X2 as a management tool. The approach 

was refined over several years of discussions and was incorporated into the Bay Delta Accord. Consistent with the 

Bay Delta Accord, the State Board reviewed this approach and adopted a standard based on it as part of the WQCP 
81

 

in 1995).

302 Thomson et al., supra note 49 (Increased water use upstream has increased salinity in the western Delta and 

Suisun Bay for as long as records exist); THE BAY INST. OF SAN FRANCISCO, FROM THE SIERRA TO THE SEA: AN 

ECOLOGICAL HISTORY OF THE SAN FRANCISCO BAY DELTA ESTUARY 175 (1998), available at

http://www.bay.org/publications/from-the-sierra-to-the-sea-the-ecological-history-of-the-san-francisco-bay-deltawaters (With the development of major reservoirs in the mid-20th century, springtime X2 changed through time in 

ways that reduced the survival and abundance of desired aquatic organisms); Jassby & Powell, supra note 30.

303 Mac Nally et al., supra note 50.

304 Kimmerer, supra note 30.

305 Id. (Not all species relying on low salinity habitat show this statistical relationship between the location of spring 

X2 and overall abundance. The delta smelt, for example, lives primarily in low salinity habitat for a large part of its 

life cycle, but shows no consistent pattern in abundance from year to year with springtime values of X2); W.J. 

Kimmerer, E.S. Gross & M.L. MacWilliams, Is the Response of Estuarine Nekton to Freshwater Flow in the San 

Francisco Estuary Explained by Variation in Habitat Volume?, 32 Estuaries & Coasts 375, 375-89 (2009). 

306 Adam Paganini et al., Metabolic Responses to Environmental Salinity in the Invasive Clam Corbula amurensis, 

AQUATIC BIOLOGY (forthcoming 2011).

307 Jassby & Powell, supra note 30.

308 SAN FRANCISCO ESTUARY PROJECT, MANAGING FRESHWATER DISCHARGE TO THE SAN FRANCISCO 

BAY/SACRAMENTO SAN JOAQUIN DELTA ESTUARY: THE SCIENTIFIC BASIS FOR AN ESTUARINE STANDARD, 127 

(1993); Jassby & Powell, supra note 30; STATE WATER RES. CONTROL BD., WATER QUALITY CONTROL PLAN FOR 

THE SAN FRANCISCO BAY/SACRAMENTO-SAN JOAQUIN DELTA ESTUARY (May 1995), available at

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/wq_control_plans/1995wqcp/1995_pl

an.shtml.

309 Frederick Feyrer et al., Modeling the Effects of Future Outflow on the Abiotic Habitat of an Imperiled Estuarine 

Fish, ESTUARIES & COASTS (2010), available at 

http://www.springerlink.com/content/d22u618x244n7j46/fulltext.pdf.

310 WATER RESOURCES DEPARTMENT, CONTRA COSTA WATER DISTRICT, HISTORICAL FRESH WATER AND SALINITY 

CONDITIONS IN THE WESTERN SACRAMENTO-SAN JOAQUIN DELTA AND SUISUN BAY: A SUMMARY OF HISTORICAL 

REVIEWS, REPORTS, ANALYSES AND MEASUREMENTS (Feb. 2010), available at

http://www.ccwater.com/salinity/HistoricalSalinityReport-2010Feb.pdf; U.S. FISH & WILDLIFE SERV., 2008

BIOLOGICAL OPINION ON THE PROPOSED COORDINATED OPERATIONS OF THE CENTRAL VALLEY PROJECT AND STATE 

WATER PROJECT (Dec. 12, 2008), available at http://www.fws.gov/sacramento/es/documents/SWPCVP_OPs_BO_12-15_final_OCR.pdf .

311 U.S. FISH & WILDLIFE SERV., supra note 310.

312 Heather Peterson & M. Vayssières, Benthic Assemblage Variability in the Upper San Francisco Estuary: a 27-

year Retrospective, 8 SAN FRANCISCO ESTUARY &WATERSHED SCI. 1, 1-27 (2010), available at 

http://www.escholarship.org/uc/item/4d0616c6; Janet Thompson, U.S. Geological Survey, Clams, Shrimp, Fish, 

Birds and Phyoplankton: Causes and Effects of Seasonal and Interannual Variation in Clam Biomass and Grazing in 

the Northern San Francisco Estuary, Presentation at 2010 Bay Delta Science Conference (2010), available at

http://www.baydeltascienceconf.com/.

313 ROBERT SCHROETER, BIOLOGY AND LONG-TERM TRENDS OF ALIEN HYDROMEDUSAE AND STRIPED BASS IN A 

BRACKISH TIDAL MARSH IN THE SAN FRANCISCO ESTUARY, PH.D. DISSERTATION, UNIV.OF CAL., DAVIS (2008).

314 Feyrer, Sommer & Slater, supra note 38; Feyrer, Nobriga & Sommer, supra note 37; Feyrer et al., supra note 

309.

315 Telephone interview with Frederick Feyrer, U.S. Bureau of Reclamation (Sept. 21, 2010) (The years since 2000 

include years that have large values for X2 (that is, the salinity gradient has moved upstream) as well as some of the 

lowest abundances for delta smelt on record, so these recent years may drive the overall relationship. Nevertheless, 

even when excluding the most recent 10 years, data still show that fall X2 conditions and adult population size 

predict subsequent young smelt abundance).

316 As noted above, water years in California are defined as October 1 through the following September 30. Water 

years in California are categorized based on the particular rainfall that year.

317 40 C.F.R. § 131.5 (Mar. 23, 1995).

318 See Water Quality Standards for the Sacramento River, San Joaquin River, and San Francisco Bay and Delta of 

the State of California,60 Fed. Reg. 4664 (Jan. 24, 1995).
82

 

319 Kimmerer, supra note 30 (The X2 standard has received continued review over the past 15 years. Although 

some of the individual species correlations had shifted over the years, the overall correlations were still valid); 

STATE WATER RES. CONTROL BD., supra note 61 (The State Board reviewed the X2 standard in 2006 and declined 

to pursue any changes to the operative criteria).

320 Kimmerer, supra note 30; Kimmerer, Gross & MacWilliams, supra note 305; BAXTER ET AL., supra note 34.

321 U.S. FISH & WILDLIFE SERV., RECOVERY PLAN FOR THE SACRAMENTO/SAN JOAQUIN DELTA NATIVE FISHES

(1996), available at http://ecos.fws.gov/docs/recovery_plan/961126.pdf.

322 See historic graphs of abundance on pages 9-10.

323 Sommer et al., supra note 25.

324 U.S. FISH & WILDLIFE SERV., supra note 310; Feyrer, supra note 309; Nobriga & Herbold, supra note 38.

325 Id.

326 Memorandum from the Reg’l Dir., Fish & Wildlife Serv., Region 8 to the Operation Manager, Bureau of 

Reclamation, Cent. Valley Operations Office, 283-84 (Dec. 12, 2008) (Water years in California are categorized 

based on the particular rainfall that year. The categories are wet, above normal, below normal, dry, and critically 

dry).

327 U.S. FISH & WILDLIFE SERV., supra note 310.

328 PBS&J, INDEPENDENT EXPERT PANEL REVIEW OF THE FAMILY FARM ALLIANCE’S INFORMATION QUALITY ACT 

CORRECTION REQUESTS (Oct. 21, 2009), available at 

http://www.fws.gov/informationquality/topics/FY2009/Family_Farm_Alliance/OCAP-IQA-APPEAL-responseexpert-review.pdf; COMM. ON SUSTAINABLE WATER & ENVTL. MGMT. IN THE CAL. BAY DELTA, A SCIENTIFIC 

ASSESSMENT OF ALTERNATIVES FOR REDUCING WATER MANAGEMENT EFFECTS ON THREATENED AND ENDANGERED 

FISHES IN CALIFORNIA’S BAY DELTA (2010), available at http://www.nap.edu/catalog.php?record_id=12881#toc.

329 Delta Smelt Consolidated Cases, No. 1:09-cv-00407 OWW DLB (E.D. Cal. Dec. 14, 2010) (The Memorandum 

Decision found that, while X2 is a valid surrogate for delta smelt habitat, the particular requirements for the location 

of X2 set forth in the 2008 Delta Smelt Biological Opinion are not legally valid and must be reconsidered by 

USFWS).

330 STATE WATER RES. CONTROL BD., FINAL REPORT ON DEVELOPMENT OF FLOW CRITERIA FOR THE SACRAMENTOSAN JOAQUIN DELTA ECOSYSTEM 190 (Aug. 3, 2010), available at

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/final_rpt.shtml.

331 CAL. DEPT. OF FISH & GAME, QUANTIFIABLE BIOLOGICAL OBJECTIVES AND FLOW CRITERIA FOR AQUATIC AND 

TERRESTRIAL SPECIES OF CONCERN DEPENDENT ON THE DELTA (Nov. 23, 2010), available at

http://www.dfg.ca.gov/water/water_rights_docs.html.

332 Central Valley Project Improvement Act (CPVIA), Pub. L. 102-575 (1992); Omnibus Public Land Management 

Act of 2009, Pub. L. 111-11(2009).

333 U.S. Fish & Wildlife Serv., Stockton Fish & Wildlife Office, http://www.fws.gov/stockton/afrp/index.cfm (last 

visited Oct. 26, 2010).

334 SAN JOAQUIN RIVER GROUP AUTHORITY, 2009 ANNUAL TECHNICAL REPORT, SAN JOAQUIN RIVER AGREEMENT 

& VERNALIS ADAPTIVE MANAGEMENT PLAN, available at http://www.sjrg.org/ (last visited Oct. 26, 2010).

335 California Department of Fish & Game, Grandtab, available at

http://www.calfish.org/Programs/AdditionalPrograms/CDFGFisheriesBranch/tabid/104/Default.aspx (last visited 

Nov. 30, 2010).

336 WILLIAM FLEENOR ET AL., ON DEVELOPING PRESCRIPTIONS FOR FRESHWATER FLOWS TO SUSTAIN DESIRABLE 

FISHES IN THE SACRAMENTO-SAN JOAQUIN DELTA 43 (2010) (Submitted to the State Water Resources Control Board 

regarding flow criteria for the Delta necessary to protect public trust resources).

337 Carl Mesick, The Effects of San Joaquin River Flows and Delta Export Rates During October on the Number of 

Adult San Joaquin Chinook Salmon that Stray, 179 FISH BULLETIN 139, 139-62 (2001).

338 Richard J. Hallock et al., Migrations of Adult King Salmon Oncorhynchus tshawytscha in the San Joaquin Delta 

as Demonstrated by the use of Sonic Tags, 151 FISH BULLETIN (1970), available at 

http://content.cdlib.org/ark:/13030/kt1p3001mh/.

339 Mesick, supra note 337.

340 California Department of Water Resources, Dayflow, http://www.water.ca.gov/dayflow/ (last visited Nov. 17, 

2010).

341 Mesick, supra note 337.

342 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., BASIN PLAN (2009), available at
83

 

http://www.waterboards.ca.gov/rwqcb5/water_issues/basin_plans/.

343 STATE WATER RES. CONTROL BD., supra note 61 at 14 (The narrative criteria states: “Water quality conditions 

shall be maintained, together with other measures in the watershed, sufficient to achieve a doubling of natural 

production of Chinook salmon from the average production of 1967-1991, consistent with the provisions of state and 

federal law”); CENT. VALLEY REG’L WATER QUALITY CONTROL BD., supra note 342 (The Central Valley Regional 

Water Quality Control Board's Basin Plan for the Sacramento and San Joaquin Basins also includes a narrative 

temperature objective as well as a numeric objective for aquatic life species, which states: "The natural receiving 

water temperature of intrastate waters shall not be altered unless it can be demonstrated to the satisfaction of the 

Regional Water Board that such alteration in temperature does not adversely affect beneficial uses....At no time or 

place shall the temperature of COLD or WARM intrastate waters be increased more than 5°F above natural 

receiving water temperature. ... In determining compliance with the water quality objectives for temperature, 

appropriate averaging periods may be applied provided that beneficial uses will be fully protected”).

344 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., AMENDMENTS TO THE 1994 WATER QUALITY CONTROL 

PLAN FOR THE SACRAMENTO RIVER AND SAN JOAQUIN RIVER BASINS III-5.0 (2005), available at

http://www.swrcb.ca.gov/rwqcb5/water_issues/basin_plans/newpages200702.pdf (“Within the legal boundaries of 

the Delta, the dissolved oxygen concentration shall not be reduced below: 7.0 mg/l in the Sacramento River (below 

the I Street Bridge) and in all Delta waters west of the Antioch Bridge; 6.0 mg/l in the San Joaquin River (between 

Turner Cut and Stockton, 1 September through 30 November); and 5.0 mg/l in all other Delta waters except for 

those bodies of water which are constructed for special purposes and from which fish have been excluded”). 

345 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., TMDL AND BASIN PLAN AMENDMENT ON DISSOLVED 

OXYGEN IN THE STOCKTON DEEP WATER SHIP CHANNEL (2005), available at 

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/san_joaquin_oxygen/index.shtml.

346 CENT. VALLEY REG’L WATER QUALITY BD., SAN JOAQUIN RIVER DISSOLVED OXYGEN TMDL – FINAL STAFF

Report (Feb. 2005), available at

http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/central_valley_projects/san_joaquin_oxygen/final_staff_report/

index.shtml.

347 CARL MESICK ET AL., ANADROMOUS FISH RESTORATION PROGRAM, U.S. FISH & WILDLIFE SERV., OFFICE OF THE 

NAT’L MARINE FISHERIES SERV., LIMITING FACTOR ANALYSES & RECOMMENDED STUDIES FOR FALL-RUN CHINOOK 

SALMON AND RAINBOW TROUT IN THE TUOLUMNE RIVER (2008).

348 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., supra note 342 at III-8 (“The natural receiving water 

temperature of intrastate waters shall not be altered unless it can be demonstrated to the satisfaction of the Regional 

Water Board that such alteration in temperature does not adversely affect beneficial uses.....At no time or place shall 

the temperature of [waters with a ‘migration of aquatic organisms’ designated use] be increased more than 5 degrees 

F above natural receiving water temperature....”).

349 CAL. DEPT. OF FISH & GAME, EFFECTS OF WATER TEMPERATURE ON ANADROMOUS SALMONIDS IN THE SAN 

JOAQUIN RIVER BASIN (Feb. 2010), available at http://www.nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=17962; 

U.S. ENVTL. PROT. AGENCY, REGION 10 GUIDANCE FOR PACIFIC NORTHWEST STATE AND TRIBAL TEMPERATURE 

WATER QUALITY STANDARDS 49 (2003), available at

http://yosemite.epa.gov/R10/water.nsf/6cb1a1df2c49e4968825688200712cb7/b3f932e58e2f3b9488256d16007d3bc

a/$FILE/TempGuidanceEPAFinal.pdf.

350 Letter from Alexis Strauss, supra note 94.

351 Letter from Maria Rea, Sacramento Area Office Supervisor, NOAA to Alexis Strauss, Water Div. Dir., U.S. EPA 

Region IX (Nov. 12, 2010).

352 STATE WATER RES. CONTROL BD., DRAFT TECHNICAL REPORT ON THE SCIENTIFIC BASIS FOR ALTERNATIVE SAN 

JOAQUIN RIVER FLOW AND SOUTHERN DELTA SALINITY OBJECTIVES (Oct. 31, 2010), available at

http://www.swrcb.ca.gov/waterrights/water_issues/programs/bay_delta/bay_delta_plan/water_quality_control_plann

ing/docs/techrpt102910.pdf.

353 These proposed dates may be delayed given resource constraints at the State Board. See STATE WATER RES.

CONTROL BD., STRATEGIC WORKPLAN FOR THE BAY-DELTA, SCHEDULE OF ELEMENT ACTIONS TABLE (Jan. 14, 

2010), available at 

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/element_actions/docs/timeline2009qtr

4.pdf.

354 STATE WATER RES. CONTROL BD., supra note 352 at 65.

355 STATE WATER RES. CONTROL BD., supra note 330 at 121 (The recommendations in this report do not take effect 
84

 

unless and until the Water Boards review and adopt them as part of their water quality control plans, basin plans, or 

water rights orders).

356 NAT’L MARINE FISHERIES SERV., BIOLOGICAL OPINION AND CONFERENCE OPINION ON THE LONG-TERM 

OPERATIONS OF THE CENTRAL VALLEY PROJECT AND STATE WATER PROJECT (JUNE 4, 2009).

357 Id. at 623-24. 

358 DELTA STEWARDSHIP COUNCIL, DELTA SCIENCE PROGRAM, THE VERNALIS ADAPTIVE MANAGEMENT PROGRAM 

(VAMP): REPORT OF THE 2010 REVIEW PANEL (MAY 13, 2010), available at

http://www.deltacouncil.ca.gov/delta_science_program/pdf/review_vamp_panel_report_final_051110.pdf.

359 Central Valley Project Improvement Act (CPVIA), Pub. L. 102-575 (1992); Omnibus Public Land Management 

Act of 2009, Pub. L. 111-11(2009) (Planning and environmental studies are currently being completed under the 

authority and funding of the CVPIA. The CVPIA included provisions for developing a restoration plan for the San 

Joaquin River and instituted a fee structure of Friant Division contractors for such activities. With the passage of 

Omnibus Public Land Management Act of 2009, the Settlement establishes the San Joaquin River Restoration Fund. 

Approximately $17 million per year from the Central Valley Project Friant Division would be deposited into the 

Fund to be available without further appropriations to implement the provisions of the Settlement). 

360 DELTA STEWARDSHIP COUNCIL, supra note 358.

361 THE BAY INST. OF SAN FRANCISCO, supra note 302.

362 Id.

363 WILLIAM J. MITSCH & JAMES G. GOSSELINK, WETLANDS 561-64 Second Edition (2nd ed. 1993).

364 LUND, supra note 23. 

365 DELTA VISION, DELTA HISTORY AND MANAGEMENT ISSUES (Nov. 27, 2006), available at 

http://deltavision.ca.gov/DeltaVisionMeetingMaterials.shtml.

366 CAL. NATURAL RES. AGENCY, STATE OF THE STATE’S WETLAND RESOURCES: 10 YEARS OF CHALLENGES AND 

PROGRESS (June 2010), available at

http://www.resources.ca.gov/docs/SOSW_report_with_cover_memo_10182010.pdf.