Co 

# W a t e r Q u a l i t y C h a l l e n g e s i n t h e S a n F r a n c i s c o B a y /
S a c r a m e n t o
- S a n J o a q u i n D e l t a E s t u a r y

United States

Environmental Protection
Agency



# U n a b r i d g e d A d v a n c e N o t i c e o f P r o p o s e d R u l e m a k i n g



# February 2011

Cover Photo : O verlooking Middle River in the Bay Delta Estuary, taken by Chris Austin

# Unabridged Advanc e Notice of Proposed Rulemaking for

Water Quality Challeng es 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 Francis co 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, revisio ns 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 ste ps 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 co mments, 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 E stuary 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. T his ANPR marks the beginning of a process to consider possible changes to EPA programs in th e 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 propos ed 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

resul t 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 Elimin ation 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 dis charging 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

onli ne 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 prote cted should be clearly identified as such and should not be submitted through www.regulations.gov or

e

- mail. R egulations.gov is an ‘‘anonymous access’’ system and EPA will not know your identity or contact information unless you provide it in the body of y our 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 T O EPA ACTIVITIES IN THE BAY DELTA ESTUAR Y

................................ ... 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 PU BLIC 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. Gen eral 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. R equest for Public Comment

................................ ................................ ...................... 50

B. Protecting Estuarine Habitat, Fish Migration Corridors and Wetlands

................................ ............ 52

1. Estuarine Habitat

................................ ................................ ................................ ...................... 52

a. Aqu atic Resource Issues

................................ ................................ ............................. 52

b. Regulatory Status

................................ ................................ ................................ ........ 54

c. Reque st 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 Resou rce 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 Con struction 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 Communit y 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 Rese arch 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 W ildlife 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 T HIS 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 2 5 million people and irrigation water to 4 million acres of farmland.

W ater quality and aquatic resources in the Bay Delta Estu ary 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) fi sh species, including delta smelt, longfin smelt, and threadfin shad, have collapsed in recent decades. Anadromous 3 

### fishes, including the winter run chinook salmon, have suffered a similar decline. The decline of these aquatic resources has generated deb ate over water resource management in the Bay Delta Estuary. Delta interests, including state and federal agencies, environmental groups, urban and agricultural water user s, commercial and recreational fishermen, and others have spent many years grappling with Bay Delta Estuary resource issues.

Con cerns regar ding Bay Delta Estuary water resource management increas ed during the 2009 water year 4 

### as water users and resource managers struggled with the effects of three years of drought. Water export limita tions caused by the drought and by restrictions imposed under the federal Endangered Species Act (ESA) 5 

### to 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 g overnment responded to th is ongoing water management crisi s 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

respon ses to Bay Delta Estuary issue s. 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 Act ion 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 volunta ry mec hanisms that may be used to restore water quality in the Bay Delta Estuary

. This ANPR is the beginning of

th is assessment.

New scientific information about the Bay Delta Estuary and its aquatic resources has substantially increased in the past few year s. This information has been developed and/or

reviewed in reports 10 

### 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 

### th e State’s Delta Vision Blue Ribbon Task Force, the Public Policy Institute of California (PPIC), the U.S. Fi sh 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 report s involve resources protected under the Clean Water Act and other EPA

programs.

EPA is using this ANPR to solicit and synthesize existing scientific informat ion 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 

### response s 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 re garding 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 Workp lan to coordinate and guide their Bay Delta Estuary activities. 15 

### Over the next several years, these s tate activities will include, among others, multiple poi nt source permit renewals, new pollutant and flow standards

for the southern Delta and lower San J oaquin River, and Total Maximum Daily Loads (TMDLs) for pesticides in the Central Valley. EPA continues to suppo rt many of the elements in the

S tate’s Workplan through technical and financial assistance.

Any EPA action taken as a result of this ANPR wi ll 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 responsib ilities, are needed to ensure that the requirement s 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 fac tual basis for EPA’s ongoing activit ies 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 Es tuary. Stakeholders and relevant government agencies are engaged in developing th e Bay Delta Conservation Plan (BDCP ) under the federal ESA and the California Natural

Communit y 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 t he 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 BD CP 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 relat ed 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 loca l agencies to help achieve the S tate's coequal goals of a reliable water supply and a restored Delta

ecosystem. To inform the Delt a 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 tha t 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 o r 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, commenter s may either reference earlier submission s (if submitted to EPA), attach earlier submission s (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. A quatic species, specific ally the

### 5



### salmonids and pelagic species suffering significant population collapse du ring the last decade, brought the Bay Delta Estuary’s water resource management issue s 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 s tate and/or f ederal 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 restrict ed in certain Bay Delta Estuary waters due to toxic blue

green 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 BA Y DELTA ESTUARY

A. Factual Background

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

– the Sacramento and

San Jo aquin 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 Californi a'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 wa ter 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 . S eve ral 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 hi gh 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, f or

### 6



### migratory and resident fish

. 25



### The fall run of chinook salmon ( Onchorhy nchus 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 (

Acip enser 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 o ne and two year old fish. 28


### However, the sensitivity of the species to these ocean c onditions is heightened by the long

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

habitats. 29 

### The loss of geneti c 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 t wo species (t hreadfin 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

smel t

.

After 2001, many of the pelagic species suffered near ly simultaneous, sharp population

### 7



### declines despit e 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 a ssociated 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 a n abrupt, significant drop in population ab undanc e , 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 Trawl 32

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 ( cal led 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 includ ing stock

- recruitment, habitat degradation, increased predation or mortality at export facilities a nd 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 i ncreases occurred in the number of fish trapped by and

colle cted 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, approximat ely 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 max im um 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 . Existin g regulatory standards are oriented toward export restrictions in the spring to protect critical migration periods during high flow months. T he 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 entrainment 36 

### 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 z ooplankton

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 co mposition 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 insecticide 41 

### 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 prim arily 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 conver ted to more effective levels of treatment in 2 007, the Sacramento plant has continued to generate ammonia/um at levels that have prompt ed

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 alga e 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



### C urrent 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 r esearch hav e 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

R esearch efforts that bega n 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 shift s , as introduced vegetati ve 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 eutr ophic 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 cubi c ya rds of gold rush mining debris; the reclamation of delta islands for human use; the dredging, deepening and

channelizat ion 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 

### E qually significant additional changes affecting the Bay Delta Estuary will challenge resource managers in the future. The antiquated levee system

- a system that h as suffered at least 160 major levee failures over the past century 54



### - 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 p resent 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 wa ter 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 an d 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 St ate, 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 n ationally 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 us e. Unde r 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 th at affect Bay Delta Estuary issues: water quality standards under Section 303(c) , point source discharge regulation under the National Pollution Discharge E liminat ion System (NPDES) program under Section

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

calculations under Sec tion 303(d), nonpoint source management programs under Section 319, and the wetlands regulatory program under Section 404. E PA also provides annual grants to California to carry out Clean Water Act pr ograms, 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 Cl ean Water Act and another under the Safe Drinking Water Act (SDWA). These

funds are added to California ’s revolving l oan programs which provide low

- interest financing for a range of water quality and environmental improvement projects. Since 2008, EPA ha s 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 Stan dards

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 t ribal standards protect public health or welfare, enhance the quality of water and serve the purposes of the Act; 59



### 4. Requ ires tha t states and t ribes review their standards every three years; and

5. Establishes the process for EPA review and approval of state and t ribal standards, including, where necessary, the promulgation of a superseding federal rule in cases where

a s ta te's or t ribe's standards are not consistent with applicable requirements of the Clean

Water Act or in situations where the Administrator determines that f ederal standards are necessary to meet the requirements of the Act.

Generally, states establish water quali ty 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 hy drological 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 t he 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’ wat er 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 recreati on, 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 w ater quality control plans to protect designated uses. The State Board’s 2006 WQCP establishes flow

crite ria while the Regional Boards’ p lans contain contaminant criteria. 60 

### The 2006 WQCP protects fish and wildlife designated uses with ten water quality c riteria 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’ p lans 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 disc harges 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 dev elopment 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 limitat ions guidelines an d 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 pollu tants 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) (in direct dischargers), EPA promulgates pretreatment standards that apply directly to those sources and are enforced by POTWs and state and f ederal

authorities. 66



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

Est uary. 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 2002 69 

### and subsequent Cea se and Desist Order 70 

### 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 stor m 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

individua l 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 W ater 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) desi gned 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 Boa rds. The Central Valley RWQ CB 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 fro m 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 are a. 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, stormw ater discharges from construction sites are permitted by individual NPDES permits issued by the Regional Boards or the California Construction General Permit 79 

### issued by

the State Board.

Stormwater Discharges Associated with Industrial Activity : Dischar ges 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 reg ulated 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 w aste 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

co ntributor 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 Sect ion 303(d)(1)(A) requires each s tate 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 s tate’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 s tate’s list, EPA must establish a list for the s tate. 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 Administrato r 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, an d a margin of safety. 87 

### Therefore, a TMDL identifies the maximum amount of a pollutant tha t 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 establi shed by s tates for listed waters. 90 

### In its review, EPA takes into consideration the legal and techni cal adequacy of the TMDL, which includes elements identified above and an implementation s chedule. If it disapproves a s tate TMDL,

EPA must establish the TMDL. 91 

### Implementation is the responsibility of sta tes. In California,

the Porter

- Cologne Water Qua lity Control Act requires that a TMDL include an implementation plan.

TMDLs established pursuant to Section 303(d)(1) for impaired waters are not self

executing. 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” un der s tate law. 93



### All of the waters within the Bay Delta Es tuary 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 oxyge n. 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 develope d 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. Th e 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 po llution: 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 de velop programs to address these challenging problems. EPA oversees these nonpoint source progra ms and provides funding to the s tate for program implementation.

California’s Porter

- Cologne Water Quality Control Act desi gnates the Water Boards as

the s tat e agencies with primary responsibility for water quality control in California and obligates them to address all discharges of waste that could affect th e quality of the waters of the

s tate, including potential nonpoint sources of pollution. The Porter

- Co logne 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 aut horities 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 progr am 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 Coast al 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 nonpoin t source program. T he 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 imple ment 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 designa ted 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 Francisc o 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 co unties. 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 l and 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 disc harge 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 sig nificantly 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, slo ughs, 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 floodpl ains 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 sew age 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 an d 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 impo rtant 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 spaw ning, forage, and refuge habitat for fish and wildlife. Clean Water Act Section 404 protects these services by limiting the dischar ge 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 lic ense 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 Se ction 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 A ct 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 Wa ter 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 Rodentici de 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 regist rant (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 effect s’’ 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 an d 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 expo sure, 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 Se ction 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 activ ities 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 p rogram 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 prov isions 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 PU BLIC COMMENT

In t his 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 a vailability 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 effect s of multiple stressors on the Bay Delta Estuary ’s aquatic

resources.

Commenters may also identify additional topics th at 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, recrea tion, 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 so urces. 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 compound s 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

toxic ity 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., glyc ogen 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 compr ehensive water quality monitoring program. Some contaminants are monitored only on an incidental or occasional basis, or not at all. C onsistent monitoring data over any particular time period is u navailable. Monitoring data is collected by multiple agen cies, with little standardization of monitoring procedure s, 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 investig ating 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 to xicity to POD species from contaminants in Bay Delta Estuary waters is unlikely to be the cause of the recent large population decline s . 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 contamina nts 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 im portant studies show high levels of toxicity to aquatic invertebrates from urban stormwater pyrethroid pesticide loadings to Bay Delta Estuary tributaries 106 

### 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 contributor s 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 pesticid es. 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 res ources 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 b elieved 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 lin k 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 (NH 3 

### ) gas and dissolved ionized ammonium (NH 4 

### +). 108 

### This document will use the term un

- ionized ammonia to refer to ammonia gas (NH 3 

### ), ammonium to refer to the ammonium ion ( NH 4 

### + ) 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

inte ractive 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 a ffect contaminant pollution (generally or for individual contamin ants)?

### 23



### ammonia nitrogen to refer to the combination of ammonia and ammonium. Un

- ionized ammonia gas is toxic to vertebrates 109 

### 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 p rimarily a function of pH but also depends on temperature and salinity. Total ammonia nitrogen is toxic to all forms of aquatic life. 110 

### Un

ionized ammonia is considerably more toxic to vertebrates than ammonium; toxicity increases with pH as the proporti on 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

low er pH 111 

### and some aquatic invertebrates may be more sensitive to ammonium than to un

ionized ammonia. 112



### Un

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

ambient total ammonia nitrogen levels can become concentrated. H igh 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 dea th. 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 nitro gen 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 (phytopla nkton), 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 c onditions 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 phyt oplankton 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 nu trients 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 diatom s, important algae in the food web

. 117



### Total ammonia nitrogen so urces 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

treatmen t plants. 118

### 24



### Total Ammonia Nitrogen and the D ecline 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 nitrog en 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. Collectiv ely, 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) toxicit y 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 fo r 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 correlat ed with decreases in fish 120 

### 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 uncle ar.

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 o n 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 t oxicity endpoints when present with other contaminants or due to differences between toxicity testing and exposure in natural environments. Multi

pollutant experiments show that copepods may be considerably more sensitive to total ammonia nitrogen concent rations 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 Es tuary 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 signif

icant variable contributing to changes that negatively impact the food supply for pela gic 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. Ammon ium 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 Estuar y 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 flagellates 133


### 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 p opulations 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 bl ue

- 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 d iatom 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 impa cted 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

correla tions 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, un

ionized ammonia or ammonium. They do, however, contain narr ative 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 th e San Fr ancisco 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 know ledge. These criteria are a guide for states, terri tories, 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 A mmonia

– 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 affi nis

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 th e 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 up dated 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 show s 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 R egional W WTP 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 Discharge s

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 lim its in NPDES permits. In the absence of numeric ammonia criteria, these permits are generally designed to meet the narrative toxicity criteria. NPDES permit limit s for ammonia are site

- specific and are based on the 1999 EPA Aquatic Life Ambient Water Qu ality 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 W WTP and the Stockton Re giona l Wastewater Control Facility (W WCF). Sacramento

R egional W WTP is the largest wastewater discharge in the Bay Delta Estuary with an average dry design flow of 181 million gallons per day. The Sacramento R egional W WTP is the greatest

source of ammoni a/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

R egional W WTP 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 Discharge s in and near Delta 157

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 (W WTP ) 8/1/2005 R5

- 2000

- 0811 181 S none

Stockton Regional Wastewater
Control Facility (W WCF) 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 0.75 3

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 3.5 2

Discovery Bay WWTP 11/30/2013 R5

- 2008

- 0179 2.1 S 4.64 1

### 29



### The Stockton R egional W WCF discharges have an average dry design flow of 55 million gallons/day, approximately one third the size of the Sacramento RWTP. The Stockton R egional

W WCF 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 R egional W WCF 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 Est uary by the Central Valley RWQC B suggests that the

Sacramento R egional W WTP 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 t otal 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 relevan t 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 onl ine.

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 suggest s site

- specific water quality standards for total ammonia nitrogen in the Bay Delta Estuary may be more effective than current

stand ards 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 a t 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 Del ta 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 ir rigation, 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 seleni um 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 th rough 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

m ore 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 p ossibility 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 concentrat ion 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 requirem ents 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 cont rollable

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 Joaq uin River flows t o restore the r iver 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 co uld 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 c hronic aquatic life criterion ( 5 micrograms/L ch ro nic exposure (four day average) measured a s 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 (chr onic) 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 CRITER I A 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 in dicator of exposure and environmental risk, because it fails to account for variables such as food web characteristics 177



### . Water column values developed in a dose

- response methodology, for example, do not take into account the relative efficiency of food we bs in concentrating selenium. An ‘efficient’ food web would be one involving a selenium

- sensitive species with a diet including a selenium

concentrating species (e.g., the clam, Corbula ). O ver the last decade EPA has been working with other agencies to e xpand 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

. High er river flows can function to transport larg e , albeit dilute, loads of selenium that settle in quieter downstream locations susceptible to food web uptake. Recent ly 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 crit eria 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 dev eloping 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 Presser

Luoma 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 Riv er 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 Joa quin 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 lo adings 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 ar e 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 seleni um 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 with in 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 wes t 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 priv ate 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 achiev e 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 en ters 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 Joaq uin 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 comp liance 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 D rain 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 wetland s 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 h ave reduced selenium loading to surface waters by approximately two

thirds. 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 w as hampered by delays in expected s tate 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 p rohibition 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 prohibitio n and water quality objectives, even if drainage treatment is no t
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 remo ve 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 thr ough 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 w ell 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 feder al 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 t o 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 characteriz e 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

- groun dwater 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

condition s 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, repellin g, 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 adverse ly 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 appl ication areas by precipitation and overland flow, irrigation runoff and return flow, POTW and stormwater discharges, and atmospheric drift.

The USG S National Water Quality Assessment Program analyzes surface waters throughout the United States for pestici des 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

ret urn 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 re lated 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 fl ows; 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 orcha rd 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; 202 

### and (5) multiple diazinon toxicity events in th e 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 documen ts 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 toxici ty 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 t o, 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 li kely 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 watershed 211 

### approximately 8, 430 tons (active ingredient) of 160 different pesticides 212 

### 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 LC5 0s (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 es tablished 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 tha t 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 impair ed 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 conc entrations 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 delt a 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 e ffect 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

pe lagic fish populations by limiting food availability or by contributing to fish toxicity through consumption. Some aquatic invertebrates are more vulnerable to pesticide toxicity 222 

### and make up a considerable portion of the diet for larval and juvenile pela gic 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 densi ties 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 a nd 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 o f 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 to xic 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 in dividual 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 betwee n 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 pesticides 232 

### has been demonstrated in species and pesticid es 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 combinations 233 

### and OP and herbicide (atrazine and cyanizine) combinations

that common ly 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

- base d 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 pesticide s 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 tes ting 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 i n 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 issue s 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 popula tions 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 toxicit y 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 fro m 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

C alifornia, 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, ou tlining 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 spe cific 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

pes ticides 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 lis ted 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 inju nction 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 pub lic 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 ESA

listed 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 permit s; 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 Est uary 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 pollutant s, 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 biolo gical 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 toxic ity 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 adversel y 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 po licies;

### 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 effec t 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

Sa cramento/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 Pest icides 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 elev ated 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 m anagement 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, focus ed 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 nume ric 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) l is t 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 Wa terways. 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 design ed 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 diazi non 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 Regul atory 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, t he Central Valley RWQCB addressed agricultural pesticide discharges into the Central Valley and Bay Delta Estu ary 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 g roups conduct water quality monitoring to determine the effect of member discharges on water quality. If specific water quality problems are identif ied in the monitoring reports, coalition g roups 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 was te 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 d raft 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 ir rigated 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

t he 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 ass ociated 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 implemen tation 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 Californi a 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 CG P 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 fo und 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 ). D iazinon and chlorpyrifos are

common ly used by landscap e 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 Ca lifornia Industrial Stormwater General Permit 270 

### ( 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 c urrent 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. Additio nally, 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

di scharges 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 discha rges 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 addres s 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, EP A 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

wat ershed 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 variou s 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 perv ious 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 h as 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 stormwat er 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 per mitting; 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 re quired 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 pesticid es to
surface waters for vector control 277 

### 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 S tate’s vector control general permit, the S tate’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 belie ved 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 effec tiveness o f regulating pes ticide 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, spe cific combinations of contaminants are of particular concern in the Bay Delta Estuary?

7. Should EPA and our s tate partners move away from evaluating isolated aquatic species for one or two pollutants, and towards evaluations of water conditions more r epresentative 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 pest icides 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 require ments 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 d etermine 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 requ irements.

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 exte nt 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 wat er 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 identifyi ng 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 consider ed 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 intro duced 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 compou nds 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

CE Cs 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 Wate r Boards have begun to include permit conditions for major POTWs to conduct special studies, technical reports and additional monitoring for CEC s 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 m ales 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 Mar sh. 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 endoc rine 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 quali ty 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 p otential 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 recommen dations 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 f irst 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 pe rsonal 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 fin dings 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 mon itoring data and subsequent decision

making 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” adop ted 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 panel 297 

### 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. Volunta ry 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 pharmaceutica ls 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 th e California Pharmacists Association, E ast B ay M unicipal U tility D istrict , C alifornia 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 long

term 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 hospi tals, 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 rev ising 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 th e 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.

P lease 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 aquati c 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 E stuarine Habitat, Fish Migration Corridors and Wetlands

1. Estuarine Habitat

a. Aquatic Resource Issues

For many species of fish and invertebrates in San Francisco Bay, oce an 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 (X2 301 

### ) plays a large role,

both historica l ly 302 

### 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 tr anspacificus ), 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 ) salinit y 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 uniqu ely 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 b road 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 abou t 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 var ied from year to year.

Since 2000, the low salinity zone in the months of September through November (fall X2) ha s 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 bot h with increased upstream abundance of invasive clams 312 

### and jellyfish 313 

### 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 ap pear 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 year 316



### (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. Pu rsuant 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 tempe rature 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

refinemen t 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, a s 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 sui te 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 down stream 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 precipit ation 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 o f 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 simul taneously 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 provisio n 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 fal l 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, b oth 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 th e 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 Septembe r and November in wet a nd 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 discusse d 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 de cision 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 s ubmitted 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 lega l 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 Microc ystis , 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, an d /or duration of low salinity habitat be changed so as to achieve ecosystem benefits for the suite of species th at use the low salinity zone? If so, how?

Is historical data on inter

- or intra

- annual frequency of variability the best basis for setting

go als 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 biolog ical connections between springtime X2 and subsequent fall X2 conditions? If so, what are they and what are their strengths and weaknesses?

4. W ould 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 Migrat ion 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 ne ar 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,

pres ently 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, lis ted 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? Wh at 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 s pring/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 River 335



### 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 th at 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 e nable 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 co ntain 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 severel y 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, tempera ture, oxygen depletion, contaminants and

diversion.

Retrospective analysis 337 

### of earlier sonic tagging data 338 

### found significant impairment of adult salmon migration to San Joaquin tributaries when total state and federal exports exceeded

three times the v olume 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

1952 1955 1958 1961 1964 1967 1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003 2006 2009

### 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 we re 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 establi sh 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 usua lly 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 implementatio n 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 combi nations 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 T MDL 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



### Chi nook salmon and steelhead have specific temperature tolerances during various life

stages, including both juvenile and adult migration. Temperature conditions at various life stages may currently be the limiting factor for successful recruitment. 347 

### The Ce ntral Valley RWQCB Basin Plan includes narrative and numeric criteria protecting, among others, the migratory aquatic organisms designated use. 348 

### Recently, C DFG 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 temp eratures in the San Joaquin, Stanislaus, Tuolumne, and

Merc ed Rivers exceeded EPA's adult c hinook migration criterion (18 degrees) for 33% to 75% of the migration season, and for certain reaches, exceeded the criterion for juve nile 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 t hese 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 sta ff report on the scientific basi s 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 Joaq uin 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 c ubic f eet per s econd 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 recommendat ion 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 th e 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 c ubic f

eet per s e cond 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 p robably 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 Act 359 

### i s 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 th e confluence of the San Joaquin and Merced Rivers. The measured

survival 360 

### and decreasing populations of salmon in the San Joaquin watershed suggest that fall

run salmon restoration to the San Joaquin River tributaries cannot succeed until the lower migrat ory 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 deci sion 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 sub mitted 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 B asin 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 i n the definition of the physical and/or chemical properties o f 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 impac ts 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 D elta 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 filtratio n 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 regula tory framework in the Bay Delta Estuary. The California State Reclamation Board estimates that approximately 130,000 new homes 364 

### are at various stages of planning and implementation within the Bay Delta Estuary, potentially converting up to 55,000 acres 365 

### o f

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 div ert 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 a cres) 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

commitmen t 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 entr ainment 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 u pstream 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 barrier s 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 sali nity 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 suffe r 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 ur ban 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

rulemakin g 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 materia l 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 exi sts 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), w hat specific activities can EPA under take to improve long

- term protection of existing and future wetlands, especially those resources on subsided islands ?

### 64



### I V. 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 pro pose or impose any requirements and instead seeks comments and suggestions for the Agency to consider in possibly developing a subsequent

p roposed rule, the various statut es and Executive Orders that normally apply to rulemaking do not apply i n this case. Should EPA subsequently determine to pursue a rulemaking, EPA will

address the statu t es 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. END NOTES

1 There is no commonly accepted precise geographic definition of the Bay Delta Estuary. The “legal Delta” is well

defined for purposes of the California Delta Protection Commission and related Cal ifornia statutes, but is not co

t erminous with the functioning estuary. This ANPR will generally refer to the larger estuary upstream of the San Francisco Bay as the Bay Delta Estuary o r 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 t he 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 rai nfall 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 C AL

. D EP ’ T OF W ATER R ES

. & B UREAU OF R ECLAMATION

, W ATER S UPPLY C ONDITIONS 2009 (Aug., 2009),

avail able at http://www.water.ca.gov/news/newsreleases/2009/081220 09martinmilligan2.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, wherea s 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 Sho rtage (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

h ttp://www.doi.gov/documents/BayDeltaMOUSigned.pdf.

9 I NTERIM F EDERAL A CTION P LAN FOR THE C ALIFORNIA B AY

- D ELTA (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 R ANDALL B AXTER

, ET AL

., P ELAGIC O RGANI SM D ECLINE P ROGRESS R EPORT : 2010 S YNTHESIS OF R ESULTS (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 pe rform oversight and review of state water quality agency activities.

14 Federal Insecticide, Fungicide and Rodenticide Act, 7 U.S.C. § 136

- 136y (2006).

15 S TATE W ATER R ES

. C ONTROL B D

., C ENT

. V ALLEY W ATER B D

., & S AN F RANCISCO B AY W ATER B D

., S TRATEGIC
W ORKPLAN FOR A CTIVITIES IN THE S AN F RANCISCO B AY /S ACRAMENTO

- S AN J OAQUIN D ELTA E STUARY (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, C AL

. F ISH & G AME C ODE § 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 habit at.

19 C AL

. W ATER C ODE § 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/d

isb_20110126_stressor _short_memo_final.pdf

. 21 D ELTA V ISION B LUE R IBBON T ASK F ORCE

, D ELTA V ISION S TRATEGIC P LAN (Oct. 2008), available at http://deltavision.ca.gov/StrategicPlanningProcess/StaffDraft/Delta_Vision_Strategic_Plan_standard_resolution.pdf ;

### 66

Estimate of federal and s tate endangered and threatened species based on discussion with U.S. Fish & Wildlife Service biologists; B AY D ELTA C ONSERVATION P LAN

, S TEERING C OMMITTEE W ORKING D RAFT (Nov. 18, 2010),

available at http://baydeltaconservationplan.com/Libraries/Whats_in_Plan/draft_BDCPreport_11292010_ClickableLinks7.pdf ; CALFED B AY D ELTA P ROGRAM

, M ULTI

- S PECIES C ONSERVATION S TRATEGY

, F INAL P ROGRAMMATIC 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 J AY L UND ET AL

., E NVISIONING F UTURES FOR THE S ACRAMENTO

- S AN J OAQUIN D ELTA (Feb. 2007), available at http://www.ppic. org/main/publication.asp?i=671; See D ELTA V ISION B LUE R IBBON T ASK F ORCE

, O UR V ISION FOR

THE C ALIFORNIA D ELTA (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 foun d in these sources).

24 J OHN E. S KINNER

, A N H ISTORICAL R EVIEW OF THE F ISH AND W ILDLIFE R ESOURCES OF THE S AN F RANCISCO B AY
A REA 226 (Cal. Dept. of Fish and Game, Water Projects Branch Rep. No. 1, 1962)

, available at http://www.estuaryarchive.org/archive/skin ner_1962/; W.A. Bennett & Peter Moyle, Where Have All the Fishes Gone? Interactive Factors Producing Fish Declines in the Sacramento

- San Joaquin Estuary, in S AN F RANCISCO

B AY : T HE E COSYSTEM 519, 519

- 42 (J.T. Hollibaugh ed., 1996); P ETER M OYLE ET AL

., 2010 C HANGING

E COSYSTEMS : A B RIEF E COLOGICAL H ISTORY OF THE D ELTA (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 F ISHERIES

, 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 har vest data are a large part of the population estimation tool, data for these three years are probably not directly comparable with earlier year ly population estimates.

28 S.T. L INDLEY ET AL

., W HAT C AUSED THE S ACRAMENTO R IVER F ALL C HINOOK S TOCK C OLLAPSE ? (20 09),

available at http://swr.nmfs.noaa.gov/media/SalmonDeclineReport.pdf.

29 Id.

30 Sommer et al., supra note 25 ; Alan Jassby & T.M. Powell, Hydrod ynamic Influences on Interannual Chlorophyll Variability in an Estuary: Upper San Francisco Bay Delta , 39 E STUARINE

, C OASTAL & S HELF S CI

. 595, 595

- 618 (1994); W.J. Kimmerer, Effects of Freshwater Flow on Abundance of Estuarine Organisms: Physical Effects o r Trophic Linkages?, 243 M ARINE E COLOGY P ROGRESS S ERIES 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 E COLOGICAL A PPLICATIONS 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 E COLOGICAL A PPLICATIONS , 167, 167

- 80 (2010).

32 The Fall Midwater Trawl is an ongoing annual survey of pel agic 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 re present “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 t he 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 B AXTER ET AL

., supra note 11 ; R ANDALL B AXTER

, ET AL

., P ELAGIC O RGANISM D ECLINE P ROGRESS R EPORT : 2007

S YNTHESIS OF R ESULTS (2008)

, available at http://www.science.calwater.ca. gov/pdf/workshops/POD/2007_IEP

POD_synthesis_report_031408.pdf; C HUCK A RMOR

, ET

. A L

, I NTERAGENCY E COLOGICAL P ROGRAM S YNTHESIS OF
2005 W ORK TO E VALUATE THE P ELAGIC O RGANISM D ECLINE IN THE U PPER S AN F RANCISCO E STUARY (2005).

35 Lenny F. Grimaldo, et al., Fact ors Affecting Fish Entrainment into Massive Water Diversions in a Tidal Freshwater Estuary: Can Fish Losses be Managed?, 29 N. A M

. J. OF F ISHERIES M GMT

. 1253, 1253

- 70 (2009).

36 Id. Entrainment refers to the diversion and probable loss of fish at the exp ort 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 C AN

. J. OF F ISHERIES &

A QUATIC S CI

. 723, 723

- 34 (2007).

38 William Bennett, Critical Assessment of the Delta Smelt Population in the San Francisco Estuary, California , 3

S AN F RANCISCO E STUARY & W ATERSHED S CI

. 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 fil e 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 S AN F RANCISCO
E STUARY & W ATERSHED S CI . 1, 1

- 17 ( 2009), available at http://repositories.cdlib.org/jmie/sfews/vol7/iss1/art3.

39 L INDLEY ET AL

., supra note 22; J AY R. L UND ET AL

., P UB

. P OLICY I NST

. OF C AL

., C OMPARING F UTURES FOR THE
S ACRAMENTO

- S AN J OAQUIN D ELTA ( 2008), available at www.ppic.org/content/pu bs/report/r_708EHR.pdf.

40 James Cloern et al., Biological Communities in San Francisco Bay Track a North Pacific Climate Shift, 37

G EOPHYSICAL R ES

. L ETTERS 1, 1

- 6 (2010 ).

41 Agency for Toxic Substances & Disease Registry (ATSDR)

, Fact Shee t: 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

env iron ment than the pyrethrins.... Pyrethrins are naturally

- occurring compounds with insecticidal properties that are found in pyrethrum extract from c ertain chrysanthemum flowers").

42 W.A. B ENNETT

, J.A. H OBBS & S.J. T EH

, I NTERPLAY OF E NVIRONMENTAL F ORCING AND G RO WTH

- S ELECTIVE

M ORTALITY IN THE P OOR Y EAR

- C LASS S UCCESS OF D ELTA S MELT 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 invert ebrates, 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 Larv al and Juvenile Delta Smelt to Dissolved Pesticides in

the Sacramento

- San Joaquin Delta, California, 39 A M

. F ISHERIES S OC ’ Y S YMP

. 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 E NVTL

. S CI

. & T ECH

. 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 E STUARINE

, C OASTA L & S HELF S CI

. 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 5 th 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

, B IOLOGICAL I NVASIONS 1, 1

- 15 (Jul. 28, 2010),

available at http://www.springerlink.com/conten t/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 C HEMOSPHERE 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 A DVANCES IN E XPERIMENTAL M ED

. & B IOLOGY 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

R EVIEWS IN F ISHERY S CI

. 21 1, 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 Tren ds for Pelagic Fishes in the Upper San Francisco Estuary , 20 E COLOGICAL A PPLICATIONS 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 P ETER M OYLE ET AL

., D ELTA S OLUTIONS C TR

. FOR W ATERSHED S CI

., U NIV

. OF C AL

., D AVIS

, H ABITAT
V ARIABILITY AND C OMPLEXITY IN THE U PPER S AN F RANCISCO E STUARY (2010), available at http://deltasolutions.ucdavis.edu/pdf/WorkingPapers/HabitatVariabilityandComplexity

- 2010Draft.pdf; B ROWN ET

AL

., IEP POD W ORKPLAN 2010 (f orthcoming 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 th e National Research Council’s Meeting on Sustainable Water and Environmental Management in the California Bay

- Delta (July 13, 2010); Anke Mueller

Solger, 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 n ote 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 S AN F RANCISCO E STUARY & W ATERSHED S CI

. 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 C OMPARING F UTURES FOR

THE S ACRAMENTO

- S AN J OAQUIN D ELTA ( T ECHNI CAL A PPENDIX D) (Pub. Policy Inst. of Cal. ed., 2008), available at http://www.ppic.org/content/pubs/other/708EHR_appendixD.pdf.

53 L UND

, supra note 23 ; Cloern supra note 50

. 54 V IVIAN G ADDIE

, M ICHAEL M IERZA & J ENNY M ARR

, L EVEE F AILUR ES IN THE S ACRAMENTO

- S AN J OAQUIN R IVER
D ELTA

, 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 Sc hwarzenegger, Governor, Cal. (Mar. 24, 2008), available at http://deltavision.ca.gov/BlueRibbonTaskForce/Communications/SLR_Followup_Lette r_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 C AL

. D EPT

. OF W ATER R ESOURCES

, M ANAGING AN U NCERTAIN F UTURE : C LIMATE C HANGE A DAPTATION
S TRATEGIES FOR C ALIFORNIA ’ S W ATER (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 A ct, 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 an d 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 standa rds should: (1) include provisions for restoring and maintaining chemical, physica l, and biological integrity of s tate and t ribal waters, (2) provide, wherever attainable, water quality for the protection and propagation of fish, shellfish, and wildlife an d recreation in and on the water (“fishable/swimmable''), and (3) consider the use and value of state and t ribal 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 S TATE W ATER R ES

. C ONTROL B D

., W ATER Q UALITY C ONTROL P LAN FOR THE S AN F RANCISCO

B AY /S ACRAMENTO

- S AN J OAQUIN D ELTA E STUARY ( 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 affe cting 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 St ockton’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 (9t h Cir. 1995).

89 40 C.F.R. §13 0.7(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. § 13 13(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 C lean W ater A ct does not “directly prohibit” release of poll utants from nonpoint sources ).

94 S TATE W ATER R ES

. C ONTROL B D

., 2010 I NTEGRATED R EPORT C LEAN W ATER A CT S ECTIONS 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 S TATE W ATER R ES

. C ONTROL B D

., C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

. & S AN F RANCISCO B AY
R EG ’ L

. W ATER Q UALITY C ONTROL B D

., 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 C lean

W ater A ct Section 404 program is conventionally referred to as the “Wetlands” program however, it appl ies to dredge and fill activities in all C lean W ater A ct jurisdictional waters. The types of waters that are jurisdictional

under the C lean W ater A ct include, but are not limited to, streams, rivers, natural ponds, lakes, impoundments, estuaries, bays, oc ean, mudflats, sloughs, and wetlands).

97 For example, fill activities that increase water velocity (armoring stream banks, straightening strea ms, 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 C lean W ater A ct 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 D ELTA S TRESSORS W ORKSHOP

, M EETING N OTICE (Dec. 30, 2010), available at http://www.deltacouncil.ca.gov/ delta_science_program/pdf/isb/d

isb_2011_01_workshop_stressors_mtg_notice_122810.pdf.

102 S TATE W ATER R ES

. C ONTROL B D

., 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) o r physical deformations, in such organisms or their offspring”).

104 M ICHAEL L. J OHNSON ET AL

., E VALUATION OF C HEMICAL

, T OXICOLOGICAL

, AND H ISTOP AT HOLOGIC AL D ATA TO

D ETERMINE THEIR R OLE IN THE P ELAGIC O RGANISM D ECLINE

, ( Apr. 20, 2010), available at http://w ww.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 E NVTL

. S CI

. T ECH . 1700, 1700

– 06 (2006).

107 D AVID O STRACH ET AL

., T HE R OLE OF C ONTAMINANTS

, WITHIN THE C ONTEXT OF M ULTIPLE S TRESSORS

, IN THE
C OLLAPSE OF THE S TRIPED B ASS P OPULATION IN THE S AN F RANCISCO E STUARY AND ITS W ATERSHED (2009)

, available at http://www.science.calwater.ca.gov/pdf/workshops/POD/POD_yr2_Ostrach_090522_report_final_djo.pdf.

108 U.S. E NVTL

. P ROT

. A GENCY

, 1999 U PDATE OF A MBIENT W ATER Q UALITY C RITERIA FOR A MMONIA (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 M ARINE P OLLUTION B UL LETIN 17, 17

- 23 (2002).

110 U.S. E NVTL

. P ROT

. A GENCY

, D RAFT 2009 U PDATE A QUATIC L IFE A MBIENT W ATER Q UALITY C RITERIA F OR
A MMONIA

– F RESHWATER (2009), available at http://water.epa.gov/scitech/swguidance/waterquality/standards/criteria/aqlife/pollutants/am monia/upload/2009_12_ 23_criteria_ammonia_2009update.pdf; U.S. E NVTL

. P ROT

. A GENCY

, supra note 108

. 111 U.S. E NVTL

. P ROT

. A GENCY

, supra note 108

. 112 I DA F LORES AT AL

., A CUTE AND C HRONIC T OXICITY OF A MMONIA ON P SEUDODIAPTOMUS F ORBESI (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 & Debor ah B. Poude, Ammonia in Aquatic Systems, U NIV

. OF

F LA

. IFAS E XTENSION

, 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 S AN F RANCISCO E STUARY & W ATERSHED S CI

. 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) E STUARIES & C OASTS 401, 401

- 16 (2006).

### 71 118 Central Valley Regional Water Quality Control Board, Ammonia Summit Summary (Aug. 18

- 19, 2009),

h ttp://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_wa ter_quality/ambient_ammonia_concentrations/o ct2010_staffupdate_ammonia.pdf.

119 A DAM B ALLARD ET AL

., I NTERAGENCY E COLOGICAL P ROGRAM

, B ACKGROUND /S UMMARY OF A MMONIA

I NVESTIGATIONS IN THE S ACRAMENTO

- S AN J OAQUIN D ELTA AND S UISUN B AY (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_co ncentrations/18aug09_am monia_summit/fullerton_pres.pdf.

122 Inge Werner et al., The Effects of Wastewater Treatment Effluent Associated Contaminants on Delta Smelt

, U NIV

. OF C AL

. D AVIS A QUATIC T OXICOLOGY L AB

. 1, 60 (2008), available at http://www.water.ca. gov/pubs/environment/interagency_ecological_program/ammonia/the_effects_of_wastewater_t
reatment_effluent

associated_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, U NIV

. OF C AL

. D AVIS A QUATIC T OXICOLOGY L AB

. 1, 63 (2009), available at http://www.science.calwater.ca.gov/pdf/workshops/POD/UCD

ATL_FINAL_REPORT_Delta%20Smelt%20Ammonia_2009.pdf; C HRISTOPHER F OE

, A DAM B ALLARD &

S TEPHANIE F ONG

, C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., N UTRIENT C ONCENTRATIONS AND

B IOLOGICAL E FFECTS IN THE S ACRAMENTO

- S AN J OAQUIN D ELTA (July 2010).

123 Werner et al., Acute Toxicity of Ammonia/um and Wastewater Treat ment Effluent

- Associated Contaminants on Delta Smelt, supra note 122

, at 63.

124 F OE

, B ALLARD & F ONG

, 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_co ncentrations/18aug09_am monia_summit/teh_pres.pdf.

126 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

, T ENTATIVE NPDES P ERMIT FOR S ACRAMENTO C OUNTY

R EGIONAL S ANITATION D ISTRICT

, R EGIONAL W ASTEWATER T REATMENT P LANT

, A TTACHMENT K (Sept. 3, 2010).

127 Id. ; Teh, supra note 125

. 128 Teh, supra note 125 ; Rand all & Tsui, supra note 109 ; F. B. Eddy, Ammonia in Estuaries and Effects on Fish , 67

J. OF F ISH B IOLOGY 1495, 1495

- 1513 (2005).

129 Jassby, supra no te 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 L IMNOLOGY & O CEANOGRAPHY (3) 580, 580

- 90 (2000).

131 Lehman, supra note 130 ; T. Brown, Phytoplankton Community Composition: The Rise of the Flagellates , 22 IEP

N EWSLETTER (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 M ARINE E COLOGY

P ROGRESS S ERIES 11, 11

- 28 (2005).

132 James Orsi, Food Habits of Several Ab undant Zooplankton Species in the Sacramento

- San Joaquin Estuary

, IEP

T ECHNICAL R EPORT 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 F RESHWATER B IOLOGY 483, 483

- 99 (1997).

135 Benni Hanson, Peter Koefoed Bjornsen & Per Juel Hansen, The Size Ratio Between Planktonic Predators and their Prey , 39(2) L IMNOLOGY & O CEANOGRAPHY 395, 395

- 403 (1994); Tom Fenchel, Marine Plankton Food

Chains , 19 A NNUAL R EVIEW OF E COL OGY E VOLUTION & S YSTEMATICS 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 E STUARIES 204

, 204

- 14 (2001).

138 Qua y Dortch, The Interaction Between Ammonium and Nitrate Uptake in Phytoplankton , 61 M ARINE E COLOGY

P ROGRESS S ERIES 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 H YDROBIOLOGIA 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 H YDROBIOLOGIA 87, 87

- 99 (2005).

143 C. E. Mioni, Does Ammonia Impact the Distribution of Harmful Algae an d 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/18aug 09_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 H YDROBIOLOGIA 187, 187

- 204 (2008).

145 S AN F RANCISCO R EG ’ L W ATER Q UALITY C ONTROL B D

., W ATER Q UALITY C ONTROL P LAN (B ASIN P LAN ) FOR THE
S AN F RANCISCO B AY B ASIN (2006), available at http://www.waterboards.ca.gov/sanfranciscobay/basin_planning.shtml.

146 U.S. E NVTL

. P ROT

. A GENCY

, supra note 108

. 147 U.S. E NVTL

. P ROT

. A GENCY

, supra note 110

. 148 Diana Engle, Larry Walker Assoc., Total Ammonia and Un

- ionized Ammonia Concentrations in the Delta: An

Examination of Ambient Concentr ations 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

ht ml.

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 F OE

, B ALLARD & F ONG

, supra note 122

. 152 U.S. E NVTL

. P ROT

. A GENCY

, D RAFT 2009 U PDATE A QUATIC L IFE A MBIENT W ATER Q UALITY C RITERIA F OR
A MMONIA

– F RESHWATER F ACTSHEET (2009), available at http://www.epa.gov/waterscience/criteria/a mmonia/factsheet2.html.

153 F OE

, B ALLARD & F ONG

, supra note 122

. 154 Letter from Walter Wadlow, Gen. Manager, Alameda County Water Dist. et al., to Kat hleen 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 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., NPDES P ERMIT R ENEWAL I SSUES A QUATIC L IFE AND
W ILDLIFE P RESERVATION S ACRAMENTO R EGIONAL C OUNTY S ANITATION D ISTRICT S ACRAMENTO R EGIONAL
W ASTEWATER T REATMENT P LANT (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 Distric t, 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. R 5

- 2002

- 0083 (2002).

159 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., W ASTE D ISCHARGE R EQUIREMENTS AND NPDES P ERMIT

FOR THE C ITY OF S TOCKTON W ASTEWATER T REATMENT C ONTROL F ACILITY NPDES P ERMIT R 5

- 2008

- 0154 (Oct. 23, 2008), available at http://www.swrcb.ca.gov /centralvalley/board_decisions/adopted_orders/san_joaquin/r5

- 2008

- 0154.pdf.

160 F OE

, B ALLARD & F ONG

, supra note 122

. 161 The term bioaccumulation is us ed 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 B IOMED ICAL & E NVTL

. S CIENCES 415, 415 (1997).

163 A. Robin Stewart et al., Food Web Pathway Determines How Selenium Affects Ecosystems: A San Francisco Bay Case Study , 38 E NVTL

. S CI .T ECH . 4519, 4519

- 26 (2004).

164 P ETER M. C HAPMAN ET AL

., E COLOGICAL A SSESSMENT OF S E LENIUM IN THE A QUATIC E NVIRONMENT 5 ( 2010) (Evidence has been mounting for several decades); See U.S. F ISH & W ILDLIFE S ERV ./ N AT ’ L M ARINE F ISHERIES
S ERV

. B IOLOGICAL O PINION ON THE C ALIFORNIA T OXICS R ULE 123 (2000) (concluded that “[N]early every major

rev iew 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 greate r 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, dri nking 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 P ESTICIDE & E NVTL

. T OXICOLOGY B RANCH

, O FFICE

OF E NVTL

. H EALTH H AZARD A SSESSMENT

, P UBLIC H EALTH G OAL FOR S ELENIUM IN D RINKING W ATER (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 s tandard, 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 he alth 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 And rew N. Cohen, Guide to the Exotic Species of San Francisco Bay (2005), http://www.exoticsguide.org (last visited Nov. 4, 2010).

168 W ILLIAM N. B ECKON & T HOMAS C. M AURER

, U.S. D EP ’ T OF THE I NTERIOR

, F ISH & W ILDLIFE S ERVICE

, S PECIES

AT R ISK FROM S ELENIUM E XPOS URE IN THE S AN F RANCISCO E STUARY , 1, 51

- 52 (Mar. 2008) (Beckon and Maurer report that little is known of risk of selenium to green sturgeon).

169 W ILLIAM N. B ECKON & T HOMAS C. M AURER

, P OTENTIAL E FFECTS OF S ELENIUM C ONTAMINATION ON

F EDERALLY

- L ISTED S PECIES R E SULTING FROM D ELIVERY OF F EDERAL W ATER TO THE S AN L UIS U NIT (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 S AN F RANCISCO E STUARY I NSTITUTE FOR THE G RASSLAND B YPASS P ROJECT O VERSIGHT C OMMITTEE

, G RASSLAND B YPASS P ROJECT A NNUAL R EPORT 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 l bs/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); S AN

### 74

F RANCISCO B AY R EG ’ L W ATER Q UALITY C ONTROL B D

., T ECHNICAL M EMORANDUM 2: N ORTH B AY S ELENIUM
D ATA S UMMARY AND S OURCE A NALYSIS 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 bio available 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, th e 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 create d 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 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., S TAFF R EPORT : T MDL FOR S ELENIUM IN THE L OWER
S AN J OAQUIN R IVER 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 S ack Dam to Vernalis. This action also set a 2 micrograms/L chronic value for the Grasslands channels and Salt Slough); See C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., 1996 B ASIN P LAN A MENDMENT (1996),

available at http://www.swrcb.ca.gov/rwqcb5/water_is sues/water_quality_studies/surface_water_ambient_monitoring/historic_r eports_and_faq_sheets/index.shtml#1996bpa (The site

- specific object ives adopted by the Regional Board for the Grasslands Marshes and Salt Slough were based in part on consideration of th e lentic conditions, but this approach has not been applied consistently throughout the watershed).

175 U.S. F ISH & W ILDLIFE S ERV

. , 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/o r foraging " ).

176 T HERESA S. P RESSER & S AMUEL N. L UOMA

, F ORECASTING S ELENIUM D ISCHARGES TO THE S AN F RANCISCO B AY

D ELTA E STUARY

, U.S. G EOLOGICAL S URVEY P ROFESSIONAL P APER 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 I NTEGRATED

E NVTL

. A SSESSMENT & M GMT . 685, 685

- 710 (2010), available at http://onlinelibrary.wiley.com/doi/10.1002/ieam.101/abstract

. 178 A MY E. K LECKNER ET AL

., U.S. G EOLOGICAL S URV EY O PEN

- F ILE R EPORT 2010

- 1252, S ELENIUM
C ONCENTRATIONS AND S TABLE I SOTOPIC C OMPOSITIONS OF C ARBON AND N ITROGEN IN THE B ENTHIC C LAM
C ORBULA AMURENSIS FRO M N ORTHERN S AN F RANCISCO B AY

, C ALIFORNIA : M AY 1995

- F EBRUARY 2010 (2010),

available at http://pubs.usgs.g ov/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 pa rt of the California Toxics Rule aquatic life criteria for listed species).

180 S TATE W ATER R ES

. C ONTROL B D

., supra note 94

. 181 S TATE W ATER R ES

. C ONTR OL B D

., W ATER Q UALITY C ONTROL P OLICY FOR D EVELOPING C ALIFORNIA ’ S C LEAN
W ATER A CT S ECTION 303( D ) L IST (Sept. 2004), available at http://www.swrcb.ca.gov/water_issues/programs/tmdl/docs/ffed_303d_listingpolicy093004.pdf.

182 S TATE W ATER R ES

. C ONTROL B D

., 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 S AN F RANCISCO B AY R EG ’ L W ATER Q UALITY C ONTROL B D

., 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 Refine ries, Order No. R2

- 2010

- 0057 (2010).

186 U.S. B UREAU OF R ECLAMATION

, S AN L UIS U NIT D RAINAGE F EATURE R E

- EVALUATION

, F INAL E NVIRONMENTAL

### 75

I MPACT S TATEMENT & R ECORD OF D ECISION 7 (Mar. 2007).

187 In this area a strict distinction between surface and groundwater, o r 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 Joaqu in 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 S an 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 equ ivalent 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 inc entive 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 S AN F RANCISCO E STUARY I NSTITUTE FOR THE G RASSLAND B YPASS P ROJECT O VERSIGHT C OMMITTEE

, supra note
17 0 (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 th e Grasslands Report). Reduction in drainage volume in reuse areas facilitates use of this ‘storage’ in lieu of surface discharges, but can concentrate selenium).

192 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., A MENDMENTS TO THE W ATER Q UALITY C ONTROL P LAN

FOR THE S ACRAMENTO R IVER AND S AN J OAQUIN R IVER B ASINS TO A DDRESS S ELENIUM C ONTROL IN THE S AN
J OAQUIN R IVER B ASIN F INAL S TAFF R EPORT 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 P RESSER & L UOMA

, supra note 176 at 20 (This selenium reservoir is such that increased applied irrigation water

does no t dil ute selenium concentration; rather, concentration increases).

195 Analysis of San Joaquin Basin selenium has a long history. See U.S. D EP ’ T OF THE I NTERIOR & C AL

. R ES

. A GENCY

, A M ANAGEMENT P LAN FOR A GRICULTURAL S UBSURFACE D RAINAGE AND R ELATED P ROBLEMS ON TH E
W ESTSIDE S AN J OAQUIN V ALLEY (Sept. 1990); U.S. B UREAU OF R ECLAMATION

, 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. G EOLOGICAL S URVEY

, P ESTICIDES IN S URFACE AND G ROUND W ATER OF THE U NITED S TATES : S UMMARY OF

THE R ESULTS OF THE N ATIONAL W ATER Q UALITY A SSESSMENT P ROGRAM (NAWQA) ( 2006), available at http:/pubs.usgs.gov/circ/20 05/1291.

198 S TATE W ATER R ES

. C ONTROL B D

., supra note 94

. 199 C HRISTOPHER F OE & V ALERIE C ONNOR

, S TAFF R EPORT C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., 1989 R ICE S EASON T OXICITY M ONITORING R ESULTS (1991), available at http://www.calwater.ca.gov/Ad min_Record/C

- 029766.pdf.

200 C HRISTOPHER F OE & V ALERIE C ONNOR

, S TAFF R EPORT C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., S AN J OAQUIN W ATERSHED B IOASSAY R ESULTS

, 1988

- 1990 (1991).

201 Kathryn Kuivila & Christopher Foe, Concentrations, Transport and Biological Effects of Dormant Spray Pesticides in the San Francisco Estuary, California , 14 E NVTL

. T OXICOLOGY & C HEMISTRY 1141, 1141

- 50 (1995).

202 Howard C. Bailey et al.

, Diazinon and Chlorpyrifos in Urban Waterways in Northern California, USA , 19

### 76

E NVTL

. T OXICOLOGY & C HEMISTRY 82, 82

- 87 (2000); V ALERIE C ONNOR

, S TAFF M EMORANDUM S TATUS OF U RBAN
S TORM R UNOFF P RODUCTS

, A LGAL T OXICITY AND H ERBICIDE L EVELS A SSOCIATED WITH U RBAN S TORM R UNOFF

, D IAZINON AND C HLORPYRIFOS D ETECTIONS IN THE S AN F RANCISCO B AY A REA

, as reported in C HRISTOPHER F OE

, S TAFF R EPORT C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., E VALUATION OF THE P OTENTIAL I MPACT OF
C ONTAMINANTS ON A QUATIC R ESOURCES IN THE C ENTRAL V ALLEY AND S ACRAMENTO

- S AN J OAQUIN D ELTA
E STUARY (1995).

203 C HRISTOPHER F OE

, L INDA D EANOVIC & D AVE H INTON

, S TAFF R EPORT C ENT

. V ALLEY R EG ’ L W ATER Q UALITY
C ONTROL B D

. T OXICITY I DENTIFICATION E VALUATIONS OF O RCHARD D ORMANT S PRAY R UNOFF (1998).

204 C HRISTOPHER F OE & R. S HEIPLINE

, S TAFF R EPORT C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., P ESTICIDES IN S UR FACE W ATER FROM A PPLICATIONS ON O RCHARDS AND A LFALFA D URING THE W INTER AND
S PRING OF 1991

- 1992 (1993).

205 Donald Weston & Michael J. Lydy, Pyrethroid Insecticides to the Sacramento

- San Joaquin Delta of California

, 44 E NVTL

. S CI

. & T ECH

. 1833, 1833

- 40 (2010).

206 S TATE W ATER R ES

. C ONTROL B D

., supra note 94

. 207 Id.

208 “Unknown toxicity” is an impairment category that documents toxic ev ents (widespread aquatic organism mortality in one location) that results from unidentified contaminants and their unidentified sources.

209 F OE & C ONNOR

, supra note 200 ; F OE & S HEIPLINE

, supra note 204 ; Weston & Lydy, supra note 205

. 210 U RBAN P ESTICIDE P OLLUTION P REVENTION P ROJECT

, P ESTICIDES OF I NTEREST FOR U RBAN S URFACE W ATER

QUALITY

, U RBAN P ESTICIDES U SE T RENDS A NNUAL R EPORT (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 ~11 00 pounds).

213 Kathryn Kuivila & Michelle Hladik, Understanding the Occurrence and Transport of Current

- Use Pesticides in the San Francisco Estuary Watershed , 6(3) S AN F RANCISCO E STUARY & W ATERSHED S CI

. 1, 1

- 19 (2008).

214 U RBAN P ESTICIDE P OLLUTION P REVENTION P ROJECT

, supra note 210

. 215 J OHNSON

, supra note 104 ; Nathaniel Schloz, Pesticides and the Decline of Pelagic Fishes in Western North America’s Largest Estuarine Ecosystem C ONSERVATION L ETTERS ( forthcoming 2011 ) ; N ATIONAL R ESEARCH
C OUNCIL

, C OMMITTEE ON S USTAINABLE W ATER AND E NVIRONMENTAL M ANAG EMENT IN THE C ALIFORNIA B AY

D ELTA

, A S CIENTIFIC A SSESSMENT OF A LTERNATIVES FOR R EDUCING W ATER M ANAGEMENT E FFECTS ON

T HREATENED AND E NDANGERED F ISHES IN C ALIFORNIA ’ S B AY D ELTA (2010), available at http://www.nap .edu/catalog.php?record_id=12881.

216 Kuivila & Moon, supra note 44

. 217 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., W ATER Q UALITY C ONTROL P LAN FOR THE S ACRAMENTO

AND S AN J OAQUIN R IVER B ASINS (2009), available at http://www.swrcb.ca.gov/centralvalley/water_is sues/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 E NVTL

. T OXICOLOGY & C HEMISTRY 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, 1 05 P ROCEEDINGS OF THE N AT ’ L A CAD

. OF S CI . 19354, 19354

- 59 (2008).

222 D ANIEL O ROS & I NGE W ERNER

, W HITE P APER FOR THE I NTERAGENCY E COLOGICAL P ROGRAM

, SFEI

C ONTRIBUTION 415, P YRETHROID I NSECTICIDES : A N A NALYSIS OF U SE P ATTERNS

, D ISTRIBUTIONS

, P OTENTIAL

T OXICITY AND F ATE IN THE S ACRAMENTO

- S AN J OAQUIN D ELTA AND C ENTRAL V ALLEY (2005), availab le at http://www.science.calwater.ca.gov/pdf/workshops/POD/CDFG_POD_Pyrethroids_White_Paper_Final_PDF.pdf.

223 P ETER M OYLE

, I NLAND F ISHES OF C ALIFORNIA 405 ( 1976) as reported in O ROS & W ERNER

, supra note 222

. 224 S. O BREBSKI

, J.J. O RSI & W. K IMMERER

, IEP T ECHNICAL R EPORT N O

. 32, L ONG T ERM T RENDS IN Z OOPLANKTON
D ISTRIBUTION AND A BUNDANCE IN THE S ACRAMENTO

- S AN J OAQUIN E STUARY (1992).

225 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., D ELTA D IAZINON AND C HLORPYRIFOS TMDL

- F INAL
B ASIN P LAN A MENDMENT S TAFF R EPORT (June 2006), available at http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/delta_op_pesticide/final_staff_rep

ort/index.sh tml; O ROS & W ERNER

, supra note 222

.

### 77 226 S TATE W ATER R ES

. C ONTROL B D

., supra note 94

. 227 U RBAN P ESTICIDE P OLLUTION P REVENTION P ROJECT

, supra note 210

. 228 O ROS & W ERNER

, 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 E NVTL

. T OXICOLOGY & C HEMISTRY 2304, 2304

- 08 (1997); Michael Lydy & K. R. Austin, Toxicity Assessment of Pesticide Mixtures Typical of the Sacramento

– San Joaquin Delta using C hironomus tentans

, 48 A RCHIVES OF E NVTL

. C ONTAMINATION & T OXICOLOGY 49, 49

– 55 (2004).

231 M. Faust et al., Additive Effects of Herbicide Combinations on Aquatic Non

- Target Organisms , 134 S CI

. OF THE
T OTAL E NV ’ 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 E NVTL

. T OXICOLOGY & C HEMISTRY 891, 891

- 900 (1991).

233 Debra Denton et al., Joint Acute Toxicity of Esfe nvalerate and Diazinon to Larval Fathead Minnows ( Pimephales promelas ), 22 E NVTL

. T OXICOLOGY & C HEMISTRY 336, 336

- 41 (2003).

234 Lydy & Austin, supra note 230

. 235 O ROS & W ERNER

, supra note 222

. 236 U RBAN P ESTICIDE P OLLUTION P REVENTION P ROJECT

, supra note 210

. 237 Kuivila & Hladik, supra note 213

. 238 Z HIMIN L U & G ENE D AVIS

, C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

. S TAFF R EPORT

, R ELATIVE

R ISK E VALUATION FOR P ESTICIDES U SED IN THE C ENTRAL V ALLEY P ESTICIDES B ASIN P LAN A MENDMENT P ROJEC T
A REA (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 Pesti cide Mixtures , 9 E COLOGY &

S OC ’ 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 wi th 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 co nsultations 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, ethop rop,fenamiphos, laled, mathamidophos, methyl parathion, phorate and phosme t (2010) have also been issued); U.S. EPA , Pesticides: Endangered Species Protection Program, http://www.epa.gov/espp/ (last visited Jan. 7 , 201 1 ) ( An updated status of the litigatio n, 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

re gularly. An updated status of the litigation, consultations, and current pesticide restrictions, along with links to the relevant administrative and court documents, is availab le 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 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., supra note 217

. 247 S AN F RANCISCO R EG ’ L W ATER Q UALITY C ONTROL B D

., S AN F RANCISCO B AY B ASIN W ATER Q UALITY C ONTROL

P LAN (2007), available at http://www.swrcb.ca.gov/sanfranciscobay/water_issues/programs/basin_plan/docs/basin_plan0 7.pdf.

248 S TATE W ATER R ES

. C ONTROL B D

., supra note 61

. 249 S TATE W ATER R ES

. C ONTROL B D

., D RAFT P OLICY FOR T OXICITY A SSESSMENT AND C ONTROL (2010), available

at http://www.waterboards.ca.gov/water_issues/programs/state_implementation_policy/docs/tox_policy.pdf.

250 S TATE W ATER R ES

. C ONTROL B D

., D RAFT S TAFF R EPORT P OLICY FOR T OXICITY A SSESSMENT AND C ONTROL (2010), available at http://www.waterboards.ca.g ov/water_issues/programs/state_implementation_policy/docs/stff_rpt_tox_policy.pdf.

251 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., supra note 217

. 252 Id.

### 78 253 Id.

254 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

. , S ACRAMENTO AND S AN J OAQUIN R IVER W ATERSHEDS

P ESTICIDE B ASIN P LAN A MENDMENT F ACT S HEET ( 2006), available at http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/central_v alley_pesticides/att2_fact .pdf.

255 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., R ELATIVE

- R ISK E VALUATION FOR P ESTICIDES U SED IN

THE C ENTRAL V ALLEY P ESTICIDE B ASIN P LAN A MENDMENT P ROJECT A REA (Feb. 2009), available at http://www.swrcb.ca.gov/centralvalley/w ater_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 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., C ENTRAL V ALLEY P ESTICIDE TMDL A ND B ASIN P LAN
A MENDMENT

- J ULY 2010 P ROJECT S TATUS U PDATE (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 S TATE W ATER R ES

. C ONTROL B D

., 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 I nformation 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_projec ts/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 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., D RAFT E NVIRONMENTAL I MPACT R EPORT I RRIGATED

L ANDS R EGULATORY P ROGRAM (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 C onditional 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 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., D RAFT E NVIRONMENTAL I MPACT S TATEMENT I RRIGATED

L ANDS R EGULATORY P ROGRAM (2010), available at http://www.swrcb.ca.gov/centralvalley/water_issues/irrigated_lands/long_term_program_development/draft_progra m_eir_july2010/index.s html.

264 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., L ONG T ERM ILRP D EVELOPMENT S UMMARY ( 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 We ston & 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) Sacr amento 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 Resou rces 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 Lahonta n R egional 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. E NVTL

. P ROT

. A GENCY

, D RAFT G ENERAL P ERMIT FOR R ESIDUALLY D ESIGNATED D ISCHARGES IN M ILFORD

, B ELLINGHAM

, AND F RANKLIN

, M ASSACHUSETTS (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 Qualit y 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 pestici des 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 include s “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 pesticid es 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

ap plies nationally, the PGP will not apply in California since EPA is not the NPDES permitting authority for the

State of California.

279 S TATE W ATER R ES

. C ONTROL B D

., N OTICE OF O PPORTUNITY TO P ROVIDE I NFORMAL C OMMENTS ON

P RELIMINARY D RAFT A DULTICIDES P ERMIT ( 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 Rel ated Effects in Human; an Overview, in C HEMICALLY I NDUCED A LTERATIONS IN S EXUAL

AND F UNCTIONAL D EVELOPMENT : T HE W ILDLIFE /H UMAN C ONNECTION 159, 159

- 74 (T. Colborn & C. Clement eds., 1992).

281 C.E. Purdom et al., Estrogenic Effects of Effluents from Sewage Treatment Works, 8 C HEM

. E COLOGY 275, 275

- 85 (1994); Susan Jobling et al., A Variety of Environmentally P ersistent Chemicals, including s ome Phthalate Plasticizers, are Weakly Estrogenic , 103 E NVTL

. H EALTH P ERSPE CTIVES 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. S CHAEFER & M.L. J OHNSON

, UC D AVIS A QUATIC E COSYSTEMS A NALYSIS L ABORATORY

, P HARMACEUTICAL

AND P ERSONAL C ARE P RODUCTS IN S URFACE W ATER

– O CCURRENCE

, F ATE AND T RANSPORT

, AND E FFECT ON
A QUATIC O RGANISMS (Oct. 2009).

284 R. Lavado et al., Site

- Specific Profiles of Estrogenic Activity in Agr icultural Areas of California’s Inland Waters

, 43 E NVTL

. S CI

. & T ECH

. 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 E NVTL

. H EALTH P ERSPE CTIVES 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 E NVTL

. H EALTH P ERSPECTIVES (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 5 th

### 80

Biennial CALFED Science Conference (Oct. 22

- 24, 2008).

287 B ENNETT

, H OBBS & T EH

, 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. E NVTL

. P ROT

. A GENCY

, G UIDELINES FOR D ERIVING N UMERICAL N ATIONAL W ATER Q UALITY C RITERIA FOR

THE P ROT ECTION OF A QUATIC O RGANISM AND T HEIR U SES (1985), available at http://water.epa.gov/scitech/swguidance/waterquality/standards/current/u pload/2009_01_13_criteria_85guidelines.p

df.

292 U.S. E NVTL

. P ROT

. A GENCY

, OW/ORD E MERGING C ONTAMINANTS W ORKGROUP

, A QUATIC L IFE C RITERIA FOR
C ONTAMINANTS OF E MERGING C ONCERN : G ENERAL C HALLENGES AND R ECOMMENDATIONS (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 C AL

. O CEAN P ROT

. C OUNCIL

, C AL

. O CEAN S CI

. T RUST

, NWRI, S AN F RANCISCO E STUARY I NST

., S. C AL

. C OASTAL W ATER R ES

. P ROJECT & U RB AN W ATER R ES

. C TR

. AT THE U NIV

. OF C AL

., I RVINE

, M ANAGING
C ONTAMINANTS OF E MERGING C ONCERN IN C ALIFORNIA : D EVELOPING P ROCESSES FOR P RIORITIZING

, M ONITORING

, AND D ETERMINING T HRESHOLDS OF C ONCERN (Sept. 2009), available at http://www.sfei.org/node/2838 (bas ed on a workshop held on April 28

- 29, 2009, in Costa Mesa, California.

296 State Water Resources Control Board, Recycled Water

– C onstituents of Emerging Concern, http://www.waterboards.ca.gov/water_issues/programs/water_recycling_policy/recycledwater_cec.sh tml (last visited Dec. 3, 2010).

297 S TATE W ATER R ES

. C ONTROL B D

., M ONITORING S TRATEGIES FOR C HEMICALS OF E MERGING C ONCERN (CEC S ) IN
R ECYCLED W ATER

– R ECOMMENDATIONS OF A S CIENTIFIC A DVISORY P ANEL ( June 25, 2010 ), available at http://www.waterboards.ca.gov/w ater_issues/programs/water_recycling_policy/docs/cec_monitoring_rpt.pdf

. 298 S TATE W ATER R ES

. C ONTROL B D

., C ONSTITUENTS OF E MERGING C ONCERN (CEC ) M ONITORING FOR R ECYCLED
W ATER

, S TAFF R EPORT (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: Advis ory 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 E COLOGICAL
A PPLICATIONS 272, 272

- 89 (1995); S AN F RANCISCO E STUARY P ROJECT

, M ANAGING F RESHWATER D ISCHARGE TO

THE S AN F RANCISCO B AY /S ACRAMENTO S AN J OAQUIN D ELTA E STUARY : T HE S CIENTIFIC B ASIS FOR AN E STUARINE
S TANDARD

, 127 (1993); P RINCIPLES FOR A GREEMENT ON B AY

- D ELTA S TANDARDS B ETWEEN THE S TATE OF
C ALIFORNIA AND THE F EDERAL G OVERNMENT (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 distr ibution 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 bott om 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 i s 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 an d 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 B ay for as long as records exist); T HE B AY I NST

. OF S AN F RAN CISCO

, F ROM T HE S IERRA TO T HE S EA : A N
E COLOGICAL H ISTORY OF THE S AN F RANCISCO B AY D ELTA E STUARY 175 (1998), available at http://www.bay.org/publications/from

- the

- sierra

- to

- the

- sea

- the

- ecological

- history

- of

- the

- san

- francisco

- bay

- delta

waters ( With the devel opment of major reservoirs in the mid

- 20 th 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 sho ws 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 Volum e?, 32 Estuaries & Coasts 375, 375

- 89 (2009).

306 Adam Paganini et al., Metabolic Responses to Environmental Salinity in the Invasive Clam Corbula amurensis

, A QUATIC B IOLOGY (forthcoming 2011).

307 Jassby & Powell, supra note 30

. 308 S AN F RANCISCO E STUARY P ROJECT

, M ANAGING F RESHWATER D ISCHARGE TO THE S AN F RANCISCO

B AY /S ACRAMENTO S AN J OAQUIN D ELTA E STUARY : T HE S CIENTIFIC B ASIS FOR AN E STUARINE S TANDARD

, 12 7 (1993); Jassby & Powell, supra note 30 ; S TATE W ATER R ES

. C ONTROL B D

., W ATER Q UALITY C ONTROL P LAN FOR

THE S AN F RANCISCO B AY /S ACRAMENTO

- S AN J OAQUIN D ELTA E STUARY (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, E STUARIES & C OASTS (2010), available at http://www.springerlink.com/content/d22u618x244n7j46/fulltext.pdf.

310 W ATER R ESOURCES D EPARTMENT

, C ONTRA C OSTA W ATER D ISTRICT

, H ISTORICAL F RESH W ATER AND S ALINITY
C ONDITIONS IN THE W ESTERN S ACRAMENTO

- S AN J OAQUIN D ELTA AND S UISUN B AY : A S UMMARY OF H ISTORICAL

R EVIEWS

, R EPORTS

, A NALYSES AND M EASUREMENTS ( Feb. 2010), available at http://www.ccwater.com/salinity/HistoricalSalinityReport

- 2010Feb.pdf; U.S. F ISH & W ILDLIFE S ERV

., 2008

B IOLOGICAL O P INION ON THE P ROPOSED C OORDINATED O PERATIONS OF THE C ENTRAL V ALLEY P ROJECT AND S TATE
W ATER P ROJECT (Dec. 12, 2008), available at http://www.fws.gov/sacramento/es/documents/SWP

CVP_OPs_BO_12

- 15_final_OCR.pdf .

311 U.S. F ISH & W ILDLIFE S ERV

., supra note 310

. 312 Heather Peterson & M. Vayssières, Benthic Assemblage Variability in the Upper San Francisco Estuary: a 27

- year Retrospective , 8 S AN F RANCISCO E STU ARY &W ATERSHED S CI . 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 an d Grazing in the Northern San Francisco Estuary, Presentation at 2010 Bay Delta Science Conference (2010), available at http://www.baydeltascienceconf.com/.

313 R OBERT S CHROETER

, B IOLOGY AND L ONG

- T ERM T RENDS OF A LIEN H YDROMEDUSAE AND S TRIPED B ASS IN A

B RACKI SH T IDAL M ARSH IN THE S AN F RANCISCO E STUARY

, P H .D. D ISSERTATION

, U NIV

. OF C AL

., D AVIS (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 th at fall X2 conditions and adult population size predict subsequent young smelt abundance )

. 316 As noted above, w ater years in California are defined as October 1 thr ough 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);

S TATE W ATER R ES

. C ONTROL B D

., supra note 61 (The State Board reviewed the X2 standard i n 2006 and declined to pursue any changes to the operative criteria).

320 Kimmerer, supra note 30 ; Kimmerer, Gross & MacWilliams, supra note 305 ; B AXTER ET AL

., supra note 34

. 321 U.S. F ISH & W ILDLIFE S ERV

., R ECOVERY P LAN FOR TH E S ACRAMENTO /S AN J OAQUIN D ELTA N ATIVE F ISHES (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. F ISH & W ILDLIFE S ERV

., 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. F ISH & W ILDLIFE S ERV

., supra note 310

. 328 PBS&J, I NDEP ENDENT E XPERT P ANEL R EVIEW OF THE F AMILY F ARM A LLIANCE ’ S I NFORMATION Q UALITY A CT
C ORRECTION R EQUESTS (Oct. 21, 2009), available at http://www.fws.gov/informationquality/topics/FY2009/Family_Farm_Alliance/OCAP

- IQA

- APPEA L

- response

expert

- review.pdf; C OMM

. ON S USTAINABLE W ATER & E NVT L

. M GM T

. IN THE C AL

. B AY D ELTA

, A S CIENTIFIC
A SSESSMENT OF A LTERNATIVES FOR R EDUCING W ATER M ANAGEMENT E FFECTS ON T HREATENED AND E NDANGERED
F ISHES IN C ALIFORNIA ’ S B AY D ELTA (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 requirement s 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 S TATE W ATER R ES

. C ONTROL B D

. , F INAL R EPORT ON D EVELOPMENT OF F LOW C RITERIA FOR THE S ACRAMENTO

S AN J OAQUIN D ELTA E COSYS TEM 190 (Aug. 3, 2010), available at http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/final_rpt.shtml.

331 C AL

. D EPT

. OF F ISH & G AME

, Q UANTIFIABLE B IOLOGICAL O BJECTIVES AND F LOW C RITERIA FOR A QUATIC AND

T ERRESTRIAL S PECIES OF C ONCERN D EPENDENT ON THE D ELTA (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 S AN J OAQUIN R IVER G ROUP A UTHORITY

, 2009 A NNUAL T ECHNICAL R EPORT

, S AN J OAQUIN R IVER A GREEMENT
& V ERNALIS A DAPTIVE M ANAG EMENT P LAN

, available at http://www.sjrg.org/ (last visited Oct. 26, 2010).

335 California D epartment of F ish & G ame, Grandtab, available at http://www.calfish.org/Programs/AdditionalPrograms/CDFGFisheriesBranch/tabid/104/Default.aspx (last visited

Nov. 30

, 2010).

336 W ILLIAM F LEENOR ET AL

., O N D EVELOPING P RESCRIPTIONS FOR F RESHWATER F LOWS TO S USTAIN D ESIRABLE

F ISHES IN THE S ACRAMENTO

- S AN J OAQUIN D ELTA 43 (2010) (Submitted to the State Water Resources Control Board regarding flow criteria for the Delta necessar y 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 F ISH B ULLETIN 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 F ISH B ULLETIN (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 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., B ASIN P LAN ( 2009 ), available at

### 83

http://www.waterboards.ca.gov/rwqcb5/water_issues/basin_plans/

. 343 S TATE W ATER R ES

. C ONTROL B D

., 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 provis ions of state and federal law”); C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., 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 st ates: "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 ti me 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 ap plied provided that beneficial uses wi ll be fully protected ” ).

344 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., A MENDMENTS TO THE 1994 W ATER Q UALITY C ONTROL

P LAN FOR THE S ACRAMENTO R IVER AND S AN J OAQUIN R IVER B ASINS 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 thr ough 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 fro m which fish have been excluded ” ).

345 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., TMDL AND B ASIN P LAN A MENDMENT ON D ISSOLVED
O XYGEN IN THE S TOCKTON D EEP W ATER S HIP C HANNEL (2005), available at http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/centr al_valley_projects/san_joaquin_oxygen/index.shtml.

346 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY B D

., S AN J OAQUIN R IVER D ISSOLVED O XYGEN TMDL

– F INAL S TAFF Report (Feb. 2005), available at http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/central_valley_projects/san_j oaquin_oxygen/final_staff_report/

index.shtml.

347 C ARL M ESICK ET AL

., A NADROMOUS F ISH R ESTORATION P ROGRAM

, U.S. F ISH & W ILDLIFE S ERV

., O FFICE OF THE
N AT ’ L M ARINE F ISHERIES S ERV

., L IMITING F ACTOR A NALYSES & R ECOMMENDED S TUDIES FOR F ALL

- R UN C HINOOK
S ALMON AND R AINBOW T ROUT IN THE T UOLUMNE R IVER (2008).

348 C ENT

. V ALLEY R EG ’ L W ATER Q UALITY C ONTROL B D

., 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 temperat ure....”).

349 C AL

. D EPT

. OF F ISH & G AME

, E FFECTS OF W ATER T EMPERATURE ON A NADROMOUS S ALMONIDS IN THE S AN
J OAQUIN R IVER B A SIN (Feb. 2010), available at http://www.nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=17962;

U.S. E NVTL

. P ROT

. A GENCY

, R EGION 10 G UIDANCE FOR P ACIFIC N ORTHWEST S TATE AND T RIBAL T EMPERATURE
W ATER Q UALITY S TANDARDS 49 (2003), available at http://yosemite.epa.g ov/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 S TATE W ATER R ES

. C ONTROL B D

. , D RAFT T ECHNICAL R EPOR T ON THE S CIENTIFIC B ASIS FOR A LTERNATIVE S AN
J OAQUIN R IVER F LOW AND S OUTHERN D ELTA S ALINITY O BJECTIVES ( 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/tec hrpt102910.pdf.

353 These proposed dates may be delayed given resource constraints at the State Board

. See S TATE W ATER R ES

. C ONTROL B D

. , S TRATEGIC W ORKPLAN FOR THE B AY

- D ELTA

, S CHEDULE OF E LEMENT A CTIONS T ABLE (Jan. 14, 2010), available at http://www.waterbo ards.ca.gov/waterrights/water_issues/programs/bay_delta/element_actions/docs/timeline2009qtr 4.pdf

. 354 S TATE W ATER R ES

. C ONTROL B D

. , supra note 352 at 65.

355 S TATE W ATER R ES

. C ONTROL B D

. , 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 N AT ’ L M ARINE F ISHERIES S ERV

. , B IOLOGICAL O PINION AND C ONFE RENCE O PINION ON T HE L ONG

- T ERM
O PERATIONS OF THE C ENTRAL V ALLEY P ROJECT AND S TATE W ATER P ROJECT (J UNE 4, 2009).

357 I d. at 6 23

- 24.

358 D ELTA S TEWARDSHIP C OUNCIL

, D ELTA S CIENCE P ROGRAM

, T HE V ERNALIS A DAPTIVE M ANAGEMENT P ROGRAM (VAMP): R EPORT OF THE 2010 R EVIEW P ANEL ( M AY 13, 20 10), 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

Jo aquin 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 pe r 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 D ELTA S TEWARDSHIP C OUNCIL

, supra note 358

. 361 T HE B AY I NST

. OF S AN F RANCISCO

, supra note 302

. 362 Id.

363 W ILL IAM J. M ITSCH & J AMES G. G OSSELINK

, W ETLANDS 561

- 64 Second Edition ( 2nd ed. 1993)

. 364 L UND

, supra note 23

. 365 D ELTA V ISION

, D ELTA H ISTORY AND M ANAGEMENT I SSUES (Nov. 27, 2006), available at http://deltavision.ca.gov/DeltaVisionMeetingMaterials.shtml

. 366 C AL

. N ATURAL R ES

. A GENCY

, S TATE OF THE S TAT E ’ S W ETLAND R ESOURCES : 10 Y EARS OF C HALLENGES AND

P ROGRESS (June 2010), available at http://www.resources.ca.gov/docs/SOSW_report_with_cover_memo_10182010.pdf.