Economic Analysis 

for Proposed

Aquatic Life and 

Aquatic-Dependent 

Wildlife Criteria for 

Selenium in the San 

Francisco Bay and 

Delta, California

Contract # EP-C-13-03

Final 

June, 2016

Prepared for:

United States Environmental 

Protection Agency

1200 Pennsylvania Ave., NW

Washington, D.C. 20460

Submitted by:

Abt Associates 

4550 Montgomery Avenue

Suite 800 North 

Bethesda, MD 20814

In Partnership with:

PG Environmental, LLC
CONTENTS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. i

Contents

Contents.................................................................................................................................... i

Exhibit List............................................................................................................................. iii

Acronym List.......................................................................................................................... iv

Executive Summary ............................................................................................................... vi

Background and Proposed Revised Criteria ................................................................ vi

Implementation ............................................................................................................ vi

Estimated Compliance Costs ...................................................................................... vii

1. Introduction..................................................................................................................1

1.1 Background...........................................................................................................1

1.2 Purpose and Scope of the Analysis.......................................................................3

1.3 Organization of Report .........................................................................................4

2. Baseline for the Analysis .............................................................................................5

2.1 Water Quality Criteria and Implementation Procedures.......................................5

2.2 Water Quality in the Bay and Delta......................................................................7

2.3 Sources of Selenium to the Bay and Delta............................................................9

2.3.1 Sediment and Soil .....................................................................................9

2.3.2 Agriculture ..............................................................................................10

2.3.3 Municipal and Industrial Dischargers.....................................................11

2.3.4 Urban Storm Water.................................................................................15

2.3.5 Atmospheric Deposition .........................................................................16

3. Proposed Revised Criteria ........................................................................................17

4. Method for Estimating Potential Costs: Point Sources..........................................19

4.1 Identification of Potentially Affected Point Source Dischargers........................19

4.2 Reasonable Potential Analysis............................................................................22

4.3 Projecting Effluent Limitations...........................................................................24

4.4 Compliance Scenarios and Costs........................................................................28

4.4.1 Potential Compliance Scenarios .............................................................28

4.4.2 Summary of Facility Control Costs ........................................................35

5. Methods for Identifying Potential Costs: Nonpoint Sources .................................38
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Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. ii

6. Summary of Results, Uncertainties, and Quality Assurance.................................39

6.1 Point Sources ......................................................................................................39

6.2 Nonpoint Sources................................................................................................39

6.3 Sensitivity Analysis, Sources of Uncertainty, and Quality Assurance ...............39

7. References...................................................................................................................43

Appendix A – Facility Analyses............................................................................................45

A.1 City of Burlingame and North Bayside Systems Unit........................................45

A.2 City of Livermore and EBDA.............................................................................47

A.3 City of Millbrae and North Bayside Systems Unit .............................................49

A.4 City of San Mateo/Foster City Estero.................................................................50

A.5 Dublin San Ramon Services District ..................................................................52

A.6 East Bay Dischargers Authority, Joint Outfall ...................................................53

A.7 East Bay Municipal Utility District, Wet Weather Facilities .............................55

A.8 East Bay Regional Park District, Hayward Marsh..............................................56

A.9 Palo Alto Regional Water Quality Control Plant................................................58

A.10 Cities of San Jose and Santa Clara......................................................................60

A.11 South Bayside System Authority, Wastewater Treatment Plant ........................62

A.12 Cities of South San Francisco, San Bruno, and the North Bayside Systems 

Unit .....................................................................................................................63

A.13 San Francisco Southeast Plant ............................................................................65

A.14 City of Sunnyvale ...............................................................................................67

A.15 Bottling Group, LLC...........................................................................................69

A.16 San Francisco International Airport....................................................................70

Appendix B - Potential Compliance Costs, 7% Discount Rate..........................................73
CONTENTS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. iii

Exhibit List

Exhibit 2-1. Baseline Bay-Delta Aquatic Life Water Quality Criteria for Selenium1............................6

Exhibit 2-2. San Francisco Bay and Delta Segments Listed as Impaired for Selenium1.......................8

Exhibit 2-3. Selenium Observations in Soils draining to South and Lower San Francisco Bay 

(Anderson 1998) ..............................................................................................................................9

Exhibit 2-4. NPDES Permitted Dischargers to the San Francisco Bay and Delta ...............................11

Exhibit 2-5. Locations of NPDES Permittees Discharging to the San Francisco Bay and Delta.........14

Exhibit 3-1. Proposed Selenium Water Quality Criteria for the San Francisco Bay and Delta.........18

Exhibit 4-1. Summary of Potentially Affected Point Source Dischargers ...........................................20

Exhibit 4-2. Locations of Potentially Affected Point Source Dischargers...........................................21

Exhibit 4-3. Summary of Selenium Reasonable Potential Analysis.....................................................22

Exhibit 4-4. Summary of Selenium Effluent Limitations.....................................................................26

Exhibit 4-5. Summary of Process Optimization Study.........................................................................30

Exhibit 4-6. Summary of Potential End-of-Pipe Treatment Technologies...........................................32

Exhibit 4-7. Summary of Potential End-of-Pipe Treatment Technologies...........................................33

Exhibit 4-8. Summary of Potential End-of-Pipe Treatment Unit Cost Curves1...................................34

Exhibit 4-9. Estimated Unit Costs of Compliance Mechanisms (2015$).............................................35

Exhibit 4-10. Treatment and Estimated Cost Increment for Affected Facilities1.................................36

Exhibit 6-1. End-of-Pipe Treatment Costs Sensitivity Analysis..........................................................41

Exhibit 6-2. Uncertainties in Analysis of Costs ...................................................................................42

Exhibit A- 1. Summary of Selenium Effluent Data: City of Burlingame WWTP ...............................46

Exhibit A- 2. Summary of Selenium Effluent Data: City of Livermore Water Reclamation Plant .....47

Exhibit A- 3. Summary of Selenium Effluent Data: City of Millbrae and North Bayside Systems Unit

.......................................................................................................................................................49

Exhibit A- 4. Summary of Selenium Effluent Data: City of San Mateo WWTP.................................51

Exhibit A- 5. Summary of Selenium Effluent Data: Dublin San Ramon Services District WWTP ....52

Exhibit A- 6. Summary of Selenium Effluent Data: East Bay Dischargers Authority Common Outfall

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

Exhibit A- 7. Summary of Selenium Effluent Data: East Bay Regional Park District.........................57

Exhibit A- 8. Summary of Selenium Effluent Data: Palo Alto Regional Water Quality Control Plant

.......................................................................................................................................................59

Exhibit A- 9. Summary of Selenium Effluent Data: San Jose/Santa Clara Water Pollution Control 

Plant ...............................................................................................................................................61

Exhibit A- 10. Summary of Selenium Effluent Data: South Bayside System Authority WWTP........62

Exhibit A- 11. Summary of Selenium Effluent Data: South San Francisco/San Bruno Water Quality 

Control Plant..................................................................................................................................64

Exhibit A- 12. Summary of Selenium Effluent Data: San Francisco Southeast Plant .........................66

Exhibit A- 13. Summary of Selenium Effluent Data: Sunnyvale Water Pollution Control Plant........68

Exhibit A- 14. Summary of Selenium Effluent Data: Bottling Group, Hayward Plant .......................69

Exhibit A- 15. Summary of Selenium Effluent Data: San Francisco International Airports, Mel Leong 

Treatment Plants............................................................................................................................71

Exhibit B-1. Treatment and Estimated Cost Increment for Affected Facilities, 7% Discount Rate.....74

Exhibit B-2: End-of-Pipe Treatment Costs Sensitivity Analysis, 7% Discount Rate ..........................76
ACRONYM LIST

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. iv

Acronym List

AMEL Average Monthly Effluent Limit

Basin Plan Regional Water Quality Control Board Water Quality Control Plan

BAT Best Available Technology Economically Achievable 

BCT Best Conventional Pollutant Control Technology 

BMP Best Management Practices

CCMP Comprehensive Conservation and Management Plan

CIWQS California Integrated Water Quality System

CTR California Toxics Rule

CVRWQCB Central Valley Regional Water Quality Control Board

CWA Clean Water Act

DNQ Detected, but Not Quantified

DW Dry-Weight Basis

ECA Effluent Concentration Allowance

EPA United States Environmental Protection Agency

gpd gallons per day

LTA Long-Term Average discharge condition

MDEL Maximum Daily Effluent Limitation

MEC Maximum Effluent Concentration

MEP Maximum Extent Practicable

μg/L micrograms per liter

μg/g micrograms per gram

mgd million gallons per day

MS4 Municipal Separate Storm Sewer Systems

North Bay North San Francisco Bay (i.e., Central San Francisco Bay, San Pablo Bay, 

Carquinez Strait, Suisun Bay, and the western part of the Delta within the 

SFRWQCB)

NPDES National Pollutant Discharge Elimination System

NTR National Toxics Rule

OAL Office of Administrative Law
ACRONYM LIST

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. v

O&M Operations and Maintenance

ppt parts per thousand

POTW Publicly Owned Treatment Works

QL Quantitation Level

Regional Water Board Regional Water Quality Control Board

RO Reverse Osmosis

RPA Reasonable Potential Analysis

SFRWQCB San Francisco Bay Regional Water Quality Control Board

SIP State Implementation Policy (Policy for Implementation of Toxics 

Standards for Inland Surface Waters, Enclosed Bays, and Estuaries of 

California)

South Bay South San Francisco Bay, Lower San Francisco Bay, and marine or 

estuarine tributary waters draining thereto

SWPPP Storm Water Pollution Prevention Plan

SWRCB State Water Resources Control Board

TMDL Total Maximum Daily Load

USGS United States Geological Survey

WQBELs Water Quality-Based Effluent Limitations

WQS Water Quality Standards

WWF Wet Weather Facilities

WWTP Wastewater Treatment Plant
EXECUTIVE SUMMARY

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. vi

Executive Summary

The United States Environmental Protection Agency (EPA) is proposing to update the 

selenium criteria applicable to marine and estuarine waters of the San Francisco Bay and 

Delta, to ensure that the criteria are protective of aquatic life and aquatic-dependent wildlife 

in the Bay and Delta. This report provides estimates of the potential incremental compliance 

actions and costs that may be associated with the proposed regulation.

Background and Proposed Revised Criteria

The proposed selenium criteria are intended to be protective of aquatic life and aquaticdependent wildlife, including federally listed threatened and endangered species in the San 

Francisco Bay and Delta. The currently applicable aquatic life water quality criteria for 

selenium in the San Francisco Bay and Delta were promulgated as part of the National 

Toxics Rule (NTR) in 1992. The criteria are based on EPA’s 1987 national aquatic life 

selenium freshwater criteria recommendations.

The proposed selenium criteria include an allowable fish tissue whole body or muscle value, 

a clam (prey) tissue value, a water column particulate concentration, a water column 

dissolved concentration, and a water column dissolved intermittent concentration. EPA used 

the whole body fish tissue criterion and a protective bird-egg tissue value, along with sitespecific hydrologic data, to model the bioaccumulation of selenium through the estuary’s 

ecosystem using the United States Geological Survey (USGS) Ecosystem-Scale Selenium 

Model. EPA used the results of the modeling to determine the protective clam (prey) tissue 

criterion and the water column particulate and dissolved criteria. The allowable selenium 

chronic water column dissolved criterion, which serves as the basis for the cost estimates in 

this document, is 0.2 micrograms per liter (μg/L). 

Implementation

Although the proposed rule does not establish any requirements directly applicable to 

regulated entities or other sources of pollution, state implementation may result in new or 

revised National Pollutant Discharge Elimination System (NPDES) permit conditions for 

point source dischargers and additional controls on nonpoint sources of pollutant loadings. 

This analysis provides information on the potential for incremental costs to be associated 

with such incremental requirements necessary to assure attainment of state water quality 

designated uses protected by the criteria in the proposed rule.

This Economic Analysis follows the State of California’s established procedures in the State 

Water Resources Control Board’s Policy for Implementation of Toxics Standards for Inland 

Surface Waters, Enclosed Bays, and Estuaries of California, and may result in a conservative 

evaluation for some point sources. However, the Regional Water Quality Control Boards 

have substantial discretion to apply other implementing permitting procedures that are 

consistent with the Policy’s requirements, and may elect to follow different methods to 

determine whether effluent limits are necessary and/or the value of the effluent limitations.
EXECUTIVE SUMMARY

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. vii

These alternative methods may result in fewer facilities requiring action and/or less stringent 

permit limitations.

Estimated Compliance Costs

EPA identified 16 point source facilities that potentially could be affected by the rule out of a 

total population of 51 facilities that discharge to waters subject to the criteria. The remaining 

facilities are covered by Total Maximum Daily Loads (TMDLs). These TMDLs were 

developed using stringent translations of narrative criteria, and EPA does not anticipate that 

facilities affected by them will be affected by the revised criteria in the proposed rule. Of the

16 potentially affected facilities, 14 are classified as major dischargers, and two are minor 

dischargers. Minor facilities are typically those that discharge less than one million gallons 

per day (mgd) and do not discharge toxics in toxic amounts. EPA did not evaluate general 

permits (e.g., for stormwater discharges) for which permit conditions typically focus on best 

management practices (BMPs) rather than pollutant-specific limits derived from numeric 

water quality criteria. 

Unlike point sources, California typically does not require nonpoint sources and municipal 

point source stormwater dischargers to achieve numeric water quality-based effluent 

limitations. The regulatory baseline for evaluating the potential impact of the proposed rule 

includes some requirements for nonpoint sources and stormwater dischargers to implement 

BMPs and wasteload allocations as part of currently adopted TMDLs, including already 

developed and adopted TMDLs for selenium in the Lower San Joaquin River watershed and 

the North San Francisco Bay. EPA assumes that the proposed rule will not result in the need 

for additional control action by nonpoint sources.

For the potentially affected point source facilities, EPA evaluated existing baseline 

conditions and conditions under the proposed rule to project the likelihood that control 

measures might be required as a consequence of the rule. Analysis of the available data for 

the affected facilities indicates that there are likely to be exceedances of projected effluent 

limits for selenium. In instances of exceedances of projected effluent limitations under the 

proposed rule, EPA determined the likely compliance scenarios and costs. Only compliance 

actions and costs that would be needed above the baseline level of controls are attributable to 

the proposed rule. For the population of potentially affected point source facilities, EPA 

estimates total incremental compliance cost of approximately $16 million per year.
INTRODUCTION

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 1

1. Introduction

The EPA is proposing to update the selenium criteria applicable to marine and estuarine 

waters of the San Francisco Bay and Delta, to ensure that the criteria are protective of aquatic 

life and aquatic-dependent wildlife in the Bay and Delta. This report provides estimates of 

the potential incremental compliance actions and costs that may be associated with the 

regulation.

1.1 Background

The Federal Water Pollution Control Act (as amended through P.L. 107–303, November 27, 

2002), also known as the Clean Water Act (CWA), sets the basic structure for regulating 

pollutant discharges into the waters of the United States. In the CWA, Congress established 

the national objective to “restore and maintain the chemical, physical, and biological integrity 

of the Nation’s waters,” and to achieve “wherever attainable, an interim goal of water quality 

which provides for the protection and propagation of fish, shellfish, and wildlife and for 

recreation in and on the water” (CWA sections 101(a) and 101(a)(2)).

The CWA establishes the basis for the current water quality standards (WQS) regulation and 

program. CWA section 303 addresses the development of state and authorized tribal WQS, 

which reflect the CWA national objectives for each water body. The core components of 

these standards are designated uses, water quality criteria, and antidegradation requirements. 

Designated uses establish the environmental objectives for a water body, while water quality 

criteria define the minimum conditions necessary to achieve those environmental objectives. 

The antidegradation program complements designated uses and criteria by providing a 

framework for maintaining and protecting water quality.

After states, authorized tribes, territories, and the District of Columbia (hereafter referred to 

as “states and authorized tribes”) designate the uses of waters under their jurisdiction, they 

must establish water quality criteria that protect those designated uses. EPA’s regulation at 

§131.11(a)(1) provides that such criteria “must be based on sound scientific rationale, and 

must contain sufficient parameters or constituents to protect the designated use.” States and 

authorized tribes must also adopt antidegradation policies to protect and maintain high 

quality waters and existing uses of all waters, and identify specific methods to implement 

those policies (§131.12).

The CWA also requires states and authorized tribes to hold public hearings once every three 

years for the purpose of reviewing applicable WQS and, as appropriate, modifying and 

adopting standards. The results of this triennial review must be submitted to EPA, and EPA 

must approve or disapprove any new or revised standards. CWA section 303(c)(4)(B) 

authorizes the Administrator to determine, even in the absence of a state submission, that a 

new or revised standard is needed to meet CWA requirements.

Under CWA section 304(a), EPA periodically publishes national criteria recommendations 

for states and authorized tribes to consider when adopting water quality criteria for particular 
INTRODUCTION

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 2

pollutants. In establishing numeric criteria, states may adopt criteria based on EPA’s CWA 

section 304(a) criteria, modified 304(a) criteria to reflect site-specific conditions, or other 

scientifically defensible methods.

EPA has developed national criteria recommendations for ambient waters as water column 

concentrations that reflect the toxicity of the pollutant to aquatic biota. Authorities can 

readily implement water column concentrations to control and limit discharges. However, for 

pollutants like selenium that accumulate in aquatic biota through diet and where toxicity is 

exhibited through dietary exposure, tissue concentrations can better represent levels of 

toxicity, particularly for higher order species if the pollutant bioaccumulates through the food 

chain. Because tissue concentrations may be difficult to implement directly, it is useful to 

translate tissue concentrations to water column values that reflect the bioaccumulation, i.e., a 

water column concentration that is related to the tissue concentration of the predator species 

of concern that is accumulating the selenium. EPA recently published a revised national 

recommended criterion for selenium (USEPA, 2016). The criterion has several elements, 

including fish tissue values (egg-ovary, whole body, and muscle) and water column values in 

dissolved selenium concentrations that reflect the allowable tissue concentrations in lentic 

and lotic water body systems. 

The currently applicable aquatic life water quality criteria for selenium in the San Francisco 

Bay and Delta are those that EPA promulgated as part of the National Toxics Rule (NTR; 57 

FR 60848, December 22, 1992; codified at 40 CFR 131.36). The aquatic life chronic criterion

value is 5.0 μg/L (total recoverable). The NTR criteria are based on EPA’s 1987 national 

aquatic life selenium freshwater criteria recommendations,1and are represented in terms of 

water column concentrations.

The revised proposed selenium criteria for the San Francisco Bay and Delta include an 

allowable fish tissue whole body or muscle value, a clam (prey) tissue value, a water column 

particulate concentration, a water column dissolved concentration and a water column 

dissolved intermittent concentration. EPA used the whole body fish tissue criterion and a 

protective bird-egg tissue value, along with site-specific hydrologic data, to model the 

bioaccumulation of selenium through the estuary’s ecosystem using the USGS EcosystemScale Selenium Model. EPA used the results of the modeling to determine the protective 

clam (prey) tissue criterion and the water column particulate and dissolved criteria. The 

allowable selenium chronic water column dissolved criterion is 0.2 μg/L. This value serves 

as the basis for estimated costs because it is expected to be the primary basis for 

implementing the criteria.

For determining total recoverable effluent limits in permits, EPA is proposing a translator 

(the ratio of dissolved to total recoverable metal) of 1 because both the dissolved and 

particulate forms of selenium may be bioavailable for uptake into the food web in the 

 

1 Ambient Water Quality Criteria for Selenium - 1987, EPA-440/5-87-008.
INTRODUCTION

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 3

estuary. The proposed criteria are applicable to the waters of the San Francisco Bay and 

Delta that are either marine or estuarine waters, i.e., waters that have a salinity of greater than 

1 part per thousand (ppt) 95% or more of the time. These waters are located within the 

jurisdictions of the San Francisco Bay Regional Water Quality Control Board (SFRWQCB) 

and the Central Valley Regional Water Quality Control Board (CVRWQCB) of the State of 

California.

1.2 Purpose and Scope of the Analysis

The purpose of this analysis is to identify, using available water quality and discharge data 

and information, the incremental compliance actions and costs that publicly owned 

wastewater treatment works (POTWs) and industrial point source dischargers may incur as a 

result of EPA’s proposed selenium criteria for the Bay and Delta. Although the proposed rule 

does not establish any requirements directly applicable to regulated entities or other sources 

of pollution, state implementation may result in new or revised NPDES permit conditions for 

point source dischargers to incorporate revised water quality-based effluent limits 

(WQBELs), based on the proposed dissolved water column selenium criterion.

Existing TMDLs in the Lower San Joaquin River watershed and in the North San Francisco 

Bay (North Bay) i.e., Central San Francisco Bay, San Pablo Bay, Carquinez Strait, Suisun 

Bay and the western part of the Delta within the SFRWQCB, already address selenium 

discharges from nonpoint sources, and EPA assumes that no additional incremental controls 

in the Delta and North Bay are necessary for nonpoint sources based on the proposed 

selenium criteria because of the stringency of the existing TMDL water quality targets. 

The South San Francisco Bay is scheduled for TMDL development by 2019, and as a result 

there may be incremental controls and costs associated with load allocations for nonpoint 

sources in the South Bay if necessary to attain standards. However, the data and information 

needed to evaluate potential control needs for nonpoint sources are very limited, and thus 

considered outside the scope of this analysis. Sources of selenium in the South Bay appear to 

originate from naturally occurring selenium in soils.

The TMDL for the North Bay also addresses selenium discharges from point sources, and 

EPA assumes that no additional incremental controls in the North Bay for point sources are 

necessary based on the proposed selenium criteria. The TMDL analysis uses fish tissue 

targets based on EPA’s proposed revised national recommended criterion (USEPA, 2015), 

including a whole body fish tissue target consistent with the proposed whole body fish tissue 

criterion for the Bay and Delta. The TMDL analysis translates the whole body fish tissue 

target into a dissolved water column value of 0.5 μg/L. The analysis indicates that because

ambient conditions are below 0.5 μg/L, dischargers may continue to discharge at current 

levels. Because current conditions in the waterbody are at or below 0.2 μg/L, it follows that 

the TMDL analysis would not need to be revised if a water column target of 0.2 μg/L, 

consistent with the proposed dissolved water column criterion, is used.
INTRODUCTION

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 4

1.3 Organization of Report

This remainder of this report is organized as follows:

Section 2: Baseline for the Analysis describes the current applicable selenium criteria and 

California State Water Resources Control Board (SWRCB) procedures for implementing the 

criteria in NPDES permits, sources of selenium to the Bay and Delta, and ongoing efforts to 

reduce and eliminate them.

Section 3: Proposed Revised Criteria outlines the proposed changes to existing selenium 

criteria.

Section 4: Method for Estimating Potential Costs: Point Sources describes the method for 

estimating compliance costs associated with baseline and revised criteria for point sources in 

terms of revisions to NPDES permits.

Section 5: Method for Identifying Potential Costs: Nonpoint Sources describes the 

method for identifying potential compliance costs associated with baseline and revised 

criteria for nonpoint sources.

Section 6: Summary of Results, Uncertainties, and Quality Assurance summarizes cost 

estimate results for point and nonpoint sources, and discusses the uncertainties associated 

with the estimates. 

Section 7: References provides the references used in the analysis.

Appendices provide data and information on individual point sources analyzed as part of this 

report, as well as results using alternative discount assumptions.
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 5

2. Baseline for the Analysis

This section describes the applicable baseline for evaluating the incremental costs associated 

with the revised selenium criteria, including current water quality criteria and associated 

implementation procedures, potential sources of selenium to the Bay and Delta, the current 

level of impairment, and listing procedures.

2.1 Water Quality Criteria and Implementation Procedures

In California, each Regional Water Quality Control Board (Regional Water Board) adopts a 

Water Quality Control Plan (hereinafter Basin Plan) that designates beneficial (designated) 

uses, establishes water quality objectives (criteria), and contains implementation programs 

and policies to achieve those objectives for all waters addressed through the plan. The

proposed criteria for selenium are applicable to the waters of the San Francisco Bay and 

Delta which are located within the jurisdictions of the SFRWQCB and the CVRWQCB. The 

Basin Plans applicable in these areas include:

 Water Quality Control Plan for the San Francisco Bay Basin (applicable to all parts of 

San Francisco Bay and the western part of the Delta, including South San Francisco Bay, 

Lower San Francisco Bay, Central San Francisco Bay, San Pablo Bay, Carquinez Strait, 

Suisun Bay, and the western portion of the Sacramento-San Joaquin Delta within the 

SFRWQCB)

 Water Quality Control Plan for the Sacramento and San Joaquin River Basins

(applicable to eastern portions of the Delta, which includes most of the Delta and the 

confluences of the Sacramento and the San Joaquin Rivers)

In addition, the SWRCB has adopted water quality control plans and policies to protect the 

water quality and to control the water resources that affect the beneficial uses of the Bay and 

Delta Estuary. The Water Quality Control Plan for the San Francisco Bay/Sacramento-San 

Joaquin Delta Estuary supplements the other Basin Plans that cover the Bay and Delta and 

establishes a comprehensive set of existing beneficial uses for all parts of the Bay and Delta. 

Existing beneficial uses in the Water Quality Control Plan for the San Francisco 

Bay/Sacramento-San Joaquin Delta Estuary for the protection of aquatic life and aquaticdependent wildlife include: 

 Warm Freshwater Habitat (WARM) – Uses of water that support warm water ecosystems 

including, but not limited to, preservation of aquatic habitats, vegetation, fish, or wildlife, 

including invertebrates.

 Cold Freshwater Habitat (COLD) – Uses of water that support cold water ecosystems 

including, but not limited to, preservation or enhancements of aquatic habitats, 

vegetation, fish, or wildlife, including invertebrates.

 Estuarine Habitat (EST) – Uses of water that support estuarine ecosystems, including, but 

not limited to, preservation or enhancement of estuarine habitats, vegetation, fish, 
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 6

shellfish, or wildlife (e.g., estuarine mammals, waterfowl, shorebirds), and the 

propagation, sustenance, and migration of estuarine organisms.

 Fish Migration (MIGR) – Uses of water that support habitats necessary for migration, 

acclimatization between fresh water and salt water, and protection of aquatic organisms 

that are temporary inhabitants of waters within the region.

 Preservation of Rare and Endangered Species (RARE) – Uses of waters that support 

habitats necessary for the survival and successful maintenance of plant or animal species 

established under state and/or federal law as rare, threatened, or endangered.

 Fish Spawning (SPWN) – Uses of water that support high quality aquatic habitats 

suitable for reproduction and early development of fish.

 Wildlife Habitat (WILD) – Uses of waters that support wildlife habitats, including, but 

not limited to, the preservation and enhancement of vegetation and prey species used by 

wildlife, such as waterfowl.

EPA promulgated the NTR on December 22, 1992. The NTR included several aquatic life 

and/or human health priority toxic pollutant criteria for various waterbodies in California, 

including aquatic life criteria for selenium in the San Francisco Bay and Delta. On May 18, 

2000, EPA promulgated the California Toxics Rule (CTR). The CTR promulgated additional 

priority toxic pollutant criteria for California and referenced the previously promulgated 

NTR criteria that were applicable in the State. Although the CTR included criteria for 

selenium, the criteria were only promulgated for areas of California other than the Bay-Delta. 

Exhibit 2-1 shows the applicable baseline (i.e., current) criteria for selenium in the San 

Francisco Bay and Delta that were promulgated in the NTR. 

Exhibit 2-1. Baseline Bay-Delta Aquatic Life Water Quality Criteria for Selenium1

Chronic Aquatic Life (4-day average; g/L) Acute Aquatic Life (1-hour average; g/L)

5 20

g/L = micrograms per liter

1. Expressed as total recoverable selenium.

On March 2, 2000, the SWRCB adopted the Policy for Implementation of Toxics Standards 

for Inland Surface Waters, Enclosed Bays, and Estuaries of California (hereinafter referred 

to as the State Implementation Policy, or SIP). The SIP became effective on April 28, 2000, 

and is used to implement priority pollutant criteria and objectives, including those 

promulgated for California in the NTR and CTR. The SWRCB adopted amendments to the 

SIP on February 24, 2005, that became effective on July 13, 2005. The SIP establishes 

implementation provisions for addressing priority pollutant criteria and objectives in NPDES 

permits for point sources. These implementation provisions include, in part, specific 

procedures for assessing the reasonable potential of point source discharges to cause or 
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 7

contribute to exceedances of applicable water quality criteria and objectives, and – in those 

instances where there is reasonable potential – specific procedures for establishing WQBELs.

2.2 Water Quality in the Bay and Delta

CWA Section 305(b) requires the State to report biennially to EPA on the condition of the 

surface water bodies throughout the State. Under Section 303(d) of the CWA, the SWRCB

and Regional Water Boards assess water quality monitoring data for California’s surface 

waters every two years to determine if pollutants are at levels that exceed applicable WQS. 

Water bodies and pollutants that exceed protective WQS are placed on the State’s 303(d) list. 

Placement on the 303(d) list of a water body that exceeds applicable WQS for a pollutant

indicates a TMDL may be necessary.

EPA has issued guidance to states about integrating the two reports. For California, this 

combined report is called the California 303(d)/305(b) Integrated Report. In accordance with 

EPA Integrated Report guidance, the SWRCB classifies each assessed water segment into 

one of five non-overlapping categories based on whether the beneficial uses are supported in

the water segment. 

 Category 5 – Available data and/or information indicate that at least one beneficial use is 

not being supported or is threatened, and a TMDL is needed. 

 Category 4 – Available data and/or information indicate that at least one beneficial use is 

not being supported or is threatened, but a TMDL is not needed.

o Category 4A – A TMDL is already established.

o Category 4B – Other required control measures are expected to result in 

attainment of an applicable water quality standard in a reasonable period of time.

o Category 4C – A water that is impacted by non-pollutant related cause(s). (e.g., 

aquatic life use is not supported due to hydrologic alteration or habitat alteration).

 Category 3 – There is insufficient available data and/or information to make any

beneficial use support determination.

 Category 2 – Data and/or information are available for some but not all beneficial uses, 

and where available, indicate that the beneficial uses are supported.

 Category 1 – All beneficial uses are supported, no use is threatened.

In California, the 303(d) list is made up of three of the Integrated Report categories, 5, 4A, 

and 4B. These categories contain water segments that are not meeting WQS or are not 

expected to meet WQS.

According to California's 2012 Water Quality Integrated Report (SWRCB, 2012), the San 

Francisco Bay and Delta were identified as impaired by selenium and listed as Category 5 

requiring a TMDL. Exhibit 2-2 lists the specific segments included on the 303(d) list for 

selenium.
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 8

Exhibit 2-2. San Francisco Bay and Delta Segments Listed as Impaired for Selenium1

Waterbody Name/Segment Expected TMDL 

Completion Date

Potential 

Sources Impairment Description

Sacramento San Joaquin 

Delta 20102

Source 

Unknown 

Affected use is one branch of 

the food chain; most sensitive 

indicator is hatchability in 

nesting diving birds, significant 

contributions from oil refineries 

(control program in place) and 

agriculture (carried downstream 

by rivers); exotic species may 

have made food chain more 

susceptible to accumulation of 

selenium; health consumption 

advisory in effect for scaup and 

scoter (diving ducks).

San Francisco Bay, Central 20102

San Francisco Bay, South 2019

San Pablo Bay 20102

Suisan Bay 20102

Carquinez Strait 20102

Central Basin 2019

Oakland Inner Harbor 2019

1. Source: California's 2012 Water Quality Integrated Report (SWRCB, 2012).

On July 24, 2015, the SFRWQCB proposed a TMDL for the North San Francisco Bay. The 

TMDL covers a small portion of the Sacramento/San Joaquin Delta (within the San 

Francisco Bay region), Suisun Bay, Carquinez Strait, San Pablo Bay, and Central Bay. On 

November 18, 2015, the SFRWQCB adopted a Basin Plan amendment that included the 

TMDL and an implementation plan (Resolution No. R2-2015-0048; Amending the Water 

Quality Control Plan for the San Francisco Bay Basin to Establish a Total Maximum Daily 

Load and Implementation Plan for Selenium in North San Francisco Bay; hereinafter, the 

North Bay TMDL). On March 15, 2016, the SWRCB approved the Basin Plan amendment. 

The Basin Plan amendment will become effective for CWA purposes upon approval by the 

State’s Office of Administrative Law (OAL), and EPA.

The SFRWQCB has initiated information collection for the development of a TMDL for the 

South San Francisco Bay. As this TMDL is in its earliest stages, it is not available for EPA to 

consider as part of the baseline or any other part of this analysis.

Selenium occurs naturally along portions of the west side of the Lower San Joaquin River 

basin, and as a result of agricultural land use practices, subsurface agricultural drainage 

discharges from this area are a major source of selenium. The CVRWQCB addressed the 

selenium through the adoption of a series of selenium TMDLs in the lower basin, including 

one for selenium in the Lower San Joaquin River. The TMDL is implemented through: 

1) prohibitions of discharge of agricultural subsurface drainage water adopted in the Basin 

Plan Amendment for the Control of Subsurface Drainage Discharges (State Water Board 

Resolution 96-078); and 2) load allocations in Waste Discharge Requirements.
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 9

2.3 Sources of Selenium to the Bay and Delta

According to the North Bay and Lower San Joaquin River selenium TMDLs, selenium in the 

San Francisco Bay and Delta mainly originates from natural sources. Although selenium can 

be released into surface waters through natural biological and geological processes, 

anthropogenic (e.g., refinery and agricultural) activities are also responsible for the dispersal 

of selenium in the estuary.

2.3.1 Sediment and Soil

Selenium is a naturally occurring element found in marine sediments of the Coast Ranges. 

Natural sources of selenium include sedimentary rocks, seleniferous soils, and selenium-rich 

mineral deposits. According to the North Bay TMDL (SFRWQCB, 2015):

“Average concentrations of selenium found in sediments and soils usually range from 

0.01 to 0.02 mg/kg with most seleniferous soils containing less than 2 mg/kg (USDHHS 

2003, Chapter 6). However, Cretaceous and Tertiary marine and sedimentary deposits 

underlying and surrounding basins such as San Joaquin Valley, and those found in 

western states are enriched in selenium. Presser (1994) identified seleniferous deposits in 

the Coast Ranges of California and the Central Valley with concentrations of selenium 

reaching 45 mg/kg and median values exceeding 6.5 mg/kg.” 

Further, soils data representing the South San Francisco Bay reported in a literature review 

conducted by Anderson (1998) for the City of San Jose Environmental Services Department 

included evidence that naturally occurring selenium is found at relatively high levels in 

bedrock units, soils, and groundwater (see Exhibit 2-3). The author notes that, at the time of

publication, no studies on processes controlling selenium transport into the South San 

Francisco Bay and Lower San Francisco Bay had been conducted. However, based on the 

presence of marine shale bedrock units which are similar to those which release selenium in 

the San Joaquin River Valley and on mercury sulfide ores which have been associated with 

selenium release in other regions, Anderson indicates that selenium migration from bedrock 

and other deposits to soils and surface water are a possibility.

Exhibit 2-3. Selenium Observations in Soils draining to South and Lower San Francisco Bay 

(Anderson 1998)

Location Observation (ppm Se) Study1

Guadalupe River Vicinity

Three samples with detected 

values (8 ppm, 2 ppm, 2 ppm) 

and an unspecified number of 

samples at <1 ppm

Kleinfelder, Inc., 1995

Gilroy 0.7 Boerngen and Shacklette, 1981

Palo Alto 0.4 Boerngen and Shacklette, 1981

Mountain View 0.4 Scott, 1995

U.S. Geometric Mean 0.26 Shacklette and Boerngen, 1984

San Mateo County 0.1 Boerngen and Shacklette, 1981
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 10

Exhibit 2-3. Selenium Observations in Soils draining to South and Lower San Francisco Bay 

(Anderson 1998)

Location Observation (ppm Se) Study1

ppm = parts per million

1. As cited in Anderson (1998).

2.3.2 Agriculture

Dry conditions in the Central Valley make irrigation necessary for nearly all commercially 

grown crops. Irrigation of the soils derived from seleniferous soils and selenium-rich mineral 

deposits leaches selenium into surface return flows, subsurface drainage, and groundwater. 

According to the TMDL for Selenium in the Lower San Joaquin River (CVRWQCB 2001):

“Subsurface drainage is produced when farmers drain the shallow groundwater from the 

root zone to protect their crops. This subsurface agricultural drainage water is high in 

naturally occurring salts and selenium. Soils and shallow groundwater with the highest 

concentrations of selenium in the SJR Basin are located in a 97,000-acre area that has 

alternately been called the Drainage Study Area, Drainage Problem Area, and most 

recently, the Drainage Project Area (DPA).”

Further, according to the North Bay TMDL (SFRWQCB 2015):

“Enrichment of selenium in soils and groundwater commonly occurs in arid and semiarid irrigated areas where application of irrigation water accelerates weathering 

processes and mobilizes naturally elevated levels of selenium in the soil profile. To 

reduce effects of salinization of agricultural lands in these areas, such as the southern 

Central Valley, large volumes of water are used to flush the excess salt and selenium that 

accumulates in the root zone (Seiler et al. 2003). Drainage of excess irrigation water

through the system of drains and canals is then necessary to prevent waterlogging of the 

soils. These drains, however, provide a conduit to carry seleniferous groundwater to 

surface water bodies and wildlife areas as it was well documented in the case of disposal 

of agricultural drainage water into the Kesterson Wildlife Rufuge. This agricultural 

drainwater is eventually conveyed to the San Joaquin River, which delivers large 

selenium loads into the Delta and North Bay. Reported selenium concentrations detected 

in irrigation drainage are very high and vary between 75 and 1400 g/L (Amweg el al. 

2003). The arid climate amplifies evaporation-related enrichment that takes place in 

lakes and wetlands resulting in selenium concentrations potentially reaching toxic 

levels.”

The North Bay TMDL, in its discussion of nonpoint sources of selenium to the North Bay 

and Delta, concluded that “...the Central Valley selenium TMDLs and restoration of 

agricultural lands to tidal systems are likely to contribute to continued reduction in selenium 

loading to the North Bay...”
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 11

2.3.3 Municipal and Industrial Dischargers

The proposed selenium criteria are applicable to marine and estuarine waters of San 

Francisco Bay and Delta. Marine and estuarine waters are those in which the salinity is 

greater than 1 ppt 95% of the time. For purposes of this analysis, this includes the waters of 

San Francisco Bay and the Sacramento-San Joaquin River Delta. Consistent with EPA’s 

November 3, 2015 memorandum regarding “Salinity from Ocean Influence on the San 

Joaquin River”, waters of the Lower San Joaquin River upstream of Vernalis are not 

considered estuarine and discharges to these waters will not be considered applicable to this 

analysis. Based on these geographical boundaries, and data contained in the California 

Integrated Water Quality System (CIWQS), Exhibit 2-4 lists the major and minor NPDES 

permittees that discharge to San Francisco Bay and Delta. 

Exhibit 2-4. NPDES Permitted Dischargers to the San Francisco Bay and Delta

NPDES 

Permit 

Number Permittee Receiving Water

Discharge 

Category Facility Type

CA0005550 Valero, Benicia Refinery Suisun Bay Major Industrial

CA0037958 Novato Sanitary District San Pablo Bay Major POTW

CA0004961 Tesoro, Golden Eagle 

Refinery

Suisun Bay Major Industrial

CA0037851 Las Gallinas Valley Sanitary 

District

Miller Creek Major POTW

CA0037702 East Bay Municipal Utility 

District

Central San Fran 

Bay

Major POTW

CA0038024 Fairfield-Suisun Sewer 

District

Boynton Slough Major POTW

CA0110116 US Navy, Treasure Island Central San Fran 

Bay

Major POTW

CA0038440 East Bay Municipal Utility 

District, Wet Weather

Richmond Inner 

Harbor (central San 

Fran Bay)

Minor POTW

CA0037621 City Of Sunnyvale Moffett Channel Major POTW

CA0037842 San Jose/Santa Clara Artesian Slough Major POTW

CA0038547 Delta Diablo New York Slough Major POTW

CA0037834 Palo Alto South San Fran 

Bay

Major POTW

CA0038091 Benicia Carquinez Strait Major POTW

CA0037800 Sonoma Valley County 

Sanitation District

Schell Slough Major POTW

CA0038130 South San Francisco-San 

Bruno

Lower San Fran 

Bay

Major POTW

CA0037532 Millbrae Lower San Fran 

Bay

Major POTW
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 12

Exhibit 2-4. NPDES Permitted Dischargers to the San Francisco Bay and Delta

NPDES 

Permit 

Number Permittee Receiving Water

Discharge 

Category Facility Type

CA0037885 Crockett Community 

Services District, Port Costa

Carquinez Strait Minor POTW

CA0030058 Bottling Group Old Alameda Creek Minor Industrial

CA0037664 San Francisco, Southeast 

Plant

Lower San Fran 

Bay

Major POTW

CA0037753 Marin County Sanitary 

District #5, Tiburon

Raccoon Strait in 

Central San Fran 

Bay

Minor POTW

CA0038539 West County Agency Central San Fran 

Bay

Major POTW

CA0037788 Burlingame Lower San Fran 

Bay

Major POTW

CA0038318 San Francisco International 

Airport, Sanitary Plant

Lower San Fran 

Bay

Major Industrial

CA0037541 San Mateo Lower San Fran 

Bay

Major POTW

CA0037711 Sewerage Agency Of 

Southern Marin

Raccoon Strait in 

Central San Fran 

Bay

Major POTW

CA0005240 C&H Sugar Company Carquinez Strait Major Industrial

CA0038067 Sausalito-Marin City 

Sanitary District

Central San Fran 

Bay

Major POTW

CA0038369 Silicon Valley Clean Water Lower San Fran 

Bay

Major POTW

CA0037796 Pinole San Pablo Bay Major POTW

CA0005789 Shell Oil, Martinez Refinery Carquinez Strait Major Industrial

CA0038628 Central Marin Sanitation 

Agency

Central San Fran 

Bay

Major POTW

CA0037826 Rodeo Sanitary District San Pablo Bay Major POTW

CA0037699 Vallejo Sanitation & Flood 

Control District

Carquinez Strait Major POTW

CA0037648 Central Contra Costa 

Sanitary District

Suisun Bay Major POTW

CA0038008 Livermore Lower San Fran 

Bay

Major POTW

CA0037613 Dublin San Ramon & 

Livermore-Amador Valley

Lower San Fran 

Bay

Major POTW

CA0037869 East Bay Dischargers 

Authority, Joint Outfall

Lower San Fran 

Bay

Major POTW
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 13

Exhibit 2-4. NPDES Permitted Dischargers to the San Francisco Bay and Delta

NPDES 

Permit 

Number Permittee Receiving Water

Discharge 

Category Facility Type

CA0038636 East Bay Regional Park 

District, Hayward Marsh

Hayward Marsh Major POTW

CA0005134 Chevron, Richmond Refinery San Pablo Bay Major Industrial

CA0005002 USS-Posco New York Slough Major Industrial

CA0038768 American Canyon North Slough Major POTW

CA0030201 Napa Salt Pond Restoration Napa Slough Minor Industrial

CA0005053 Phillips 66, San Francisco 

Refinery, Rodeo

San Pablo Bay Major Industrial

CA0037427 Marin County Sanitary 

District #5, Paradise Cove

Central San Fran 

Bay

Minor POTW

CA0037575 Napa Sanitation District Napa River Major POTW

CA0037810 Petaluma Petaluma River Major POTW

CA0037770 Mt. View Sanitary District Peyton Slough Major POTW

CA0030198 Exploratorium San Fran Bay 

Central Basin

Minor Industrial

CA0029904 Crockett Cogeneration Carquinez Strait Minor Industrial

CA0006165 ECOSERVICES (Formerly 

SOLVAY [Formerly 

RHODIA])

Carquinez Strait Major Industrial

CA0004880 GenOn Pittsburg Power 

Plant

Suisun Bay Major Industrial
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 14

Exhibit 2-5. Locations of NPDES Permittees Discharging to the San Francisco Bay and Delta

As shown in Exhibit 2-5, there are no point sources that discharge into the portion of the 

Delta that would be subject to the proposed selenium criteria. Further, according to the

TMDL for the Lower San Joaquin River (CVRWQCB, 2001), there are no municipal or 

industrial sources of selenium. 

The North Bay TMDL (SFRWQCB, 2015) states that petroleum refineries are the largest 

source of selenium in the North Bay among point sources. However, efforts by the petroleum 

refineries in the “...1990s and the change in speciation in effluent from more bioavailable 

selenite to less bioavailable dissolved selenium forms dominated by selenate have 

significantly lessened the impact of the refineries’ discharge on water quality.” Therefore the 

wasteload allocations for the petroleum refineries require them to discharge no more than 

their current loadings to the North Bay. Other municipal and industrial point sources are not 
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 15

considered to be a significant source of selenium, and the wasteload allocations for the 

remaining point sources (other industrial facilities and POTWs) in the North Bay were also 

established at no more than their current selenium loadings. 

As shown in Exhibit 2-4, 14 POTWs and two industrial dischargers are the only point 

sources discharging into the Lower San Francisco Bay, South San Francisco Bay, and marine 

or estuarine tributary waters draining thereto (South Bay). 

2.3.4 Urban Storm Water

Stormwater discharges are generated by precipitation and runoff from land, pavements, 

building rooftops, and other surfaces. Storm water from municipal and industrial areas may 

contribute toxic pollutants to surface waters. California regulates stormwater discharges from 

municipal separate storm sewer systems (MS4s) through individual and general permits. 

Under Phase I, NPDES stormwater permits for medium (serving between 100,000 and 

250,000 people) and large (serving 250,000 people) municipalities have been issued by the 

Regional Water Boards. In several instances, NPDES permits are issued to a group of copermittees encompassing an entire metropolitan area (e.g., counties). 

In 2003 the SWRCB issued a General Permit for the Discharge of Storm Water from Small 

MS4s (Water Quality Order No. 2003-0005-DWQ) to provide permit coverage for Phase II 

smaller municipalities (population less than 100,000), including non-traditional small MS4s 

(e.g., military bases, public campuses). The Phase II Small MS4 General Permit covers Phase 

II Permittees state-wide. The Phase II General Permit (Order No. 2013-001 DWQ) was 

reissued in February 2013 by the SWRCB.

In the San Francisco Bay area, the SFRWQCB originally issued county-wide individual 

NPDES permits to all Phase I MS4s. In 2009, the SFRWQCB reissued all the county-wide 

municipal stormwater permits as one Municipal Regional Stormwater NPDES Permit to 

regulate stormwater discharges from municipalities and local agencies in Alameda, Contra 

Costa, San Mateo, and Santa Clara counties, and the cities of Fairfield, Suisun City, and 

Vallejo. On November 18, 2015, the Municipal Regional Stormwater NPDES Permit was 

reissued by the SFRWQCB. 

The CVRWQCB is currently working with Phase I and II permittees to develop a Regionwide MS4 permit (Region-wide Permit) that could address both Phase I and II MS4 

permittees within the Central Valley region. Currently, each Phase I MS4 permittee is 

covered under an individual permit issued by the CVRWQCB. Phase II MS4 permittees are 

currently covered under the SWRCB Phase II General Order. The single Region-wide MS4 

permit would promote greater watershed/drainage shed coordination and water quality 

measure protections, and promote greater program implementation efficiencies.

The Phase I MS4 permits require the discharger to develop and implement a Stormwater 

Management Plan/Program with the goal of reducing the discharge of pollutants to the 

maximum extent practicable (MEP). MEP is the performance standard specified in Section 
BASELINE FOR THE ANALYSIS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 16

402(p) of the CWA. The management programs specify what BMPs will be used to address 

certain program areas. The program areas include public education and outreach; illicit 

discharge detection and elimination; construction and post-construction; and good 

housekeeping for municipal operations. In general, medium and large municipalities are 

required to conduct monitoring.

The SWRCB also regulates the stormwater discharges from industrial and construction sites. 

In April 2014, the SWRCB adopted the General Permit for Stormwater Discharges 

Associated with Industrial Activities (Order 2014-0057-DWQ). The Industrial General 

Permit regulates stormwater discharges associated with several broad categories of industrial 

activities, and requires the implementation of Best Available Technology Economically 

Achievable (BAT) and Best Conventional Pollutant Control Technology (BCT) to achieve 

performance standards. The Industrial General Permit also requires permittees to develop a 

Stormwater Pollution Prevention Plan (SWPPP) and monitoring plan. The SWPPP must

identify the site-specific sources of pollutants and describe the measures at the facility 

applied to reduce stormwater pollution.

In September 2009, the SWRCB adopted the General Permit for Discharges of Storm Water 

Associated with Construction Activity Construction General Permit (Order 2009-0009-

DWQ; as amended by Orders 2010-0014-DWQ and 2012-006-DWQ). Dischargers whose 

projects disturb one or more acres of soil or whose projects disturb less than one acre but are 

part of a larger common plan of development that in total disturbs one or more acres, are 

required to obtain coverage under the Construction General Permit. Construction activity 

subject to this permit includes clearing, grading and disturbances to the ground such as 

stockpiling, or excavation. The Construction General Permit requires the development and 

implementation of a SWPPP, including BMPs the discharger will use to protect stormwater 

runoff and the placement of those BMPs. Additionally, the SWPPP must contain a visual 

monitoring program, and a chemical monitoring program for "non-visible" pollutants to be 

implemented if there is a failure of BMPs.

2.3.5 Atmospheric Deposition

According to the North Bay TMDL (SFRWQCB 2015), atmospheric deposition (both wet 

and dry) is considered a very minor selenium source.
PROPOSED REVISED CRITERIA

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 17

3. Proposed Revised Criteria

The proposed selenium criteria are intended to be protective of aquatic life and aquaticdependent wildlife, including federally listed threatened and endangered species in the San 

Francisco Bay and Delta. 

The USGS Ecosystem-Scale Selenium Model integrates two general categories of variables: 

those attributable to species (i.e., general food webs, representative species, critical life 

stages, diet mixes for representative species, trophic transfer factors, and effect 

concentrations), and those related to the aquatic environment (i.e., partitioning coefficient, 

hydrologic water year type/condition, and flow season).

EPA used the Ecosystem-Scale Selenium Model to model two critical food webs present in 

the estuary, a clam-based web and an insect-based web, to determine protective dissolved, 

particulate and prey-tissue selenium values. Endpoints included estimated selenium tissue 

effect concentration values for several important species (or surrogate species) known to be 

living in the estuary modeled through the species’ food web. 

The results of EPA’s modeling form the basis for the proposed criteria shown in Exhibit 3-1. 

All criteria are chronic values; the values reflect protective levels of selenium through dietary 

exposure, which reflects a long term or chronic exposure.
PROPOSED REVISED CRITERIA

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 18

Exhibit 3-1. Proposed Selenium Water Quality Criteria for the San Francisco Bay and 

Delta

Media 

Type Tissue Water Column1

Criteria

Dissolved Particulate

Fish

Whole Body 

or Muscle

Clam Chronic Intermittent Exposure2 Chronic

Magnitude

8.5 μg/g dw

whole body

or

11.3 μg/g dw 

muscle

15 μg/g dw 0.2 μg/L

WQCint =

0.2 μg/L − Cbkgrnd(1 − f int)

f int

1 μg/g dw

Duration Instantaneous 

measurement

Instantaneous 

measurement

30 days Number of days/month with an 

elevated concentration 30 days

Frequency Not to be 

exceeded

Not to be 

exceeded

Not more 

than once 

in three 

years

Not more than once in three years

Not more 

than once in 

three years

dw = dry-weight basis

μg/g = micrograms per gram

μg/L = micrograms per liter

1 Dissolved and particulate water column values are based on total selenium (includes all oxidation states, i.e., 

selenite, selenate, organic selenium and any other forms) in water. 

2 Cbkgrnd is the average background selenium concentration in μg/L. fint is the fraction of any 30-day period 

during which elevated selenium concentrations occur. fint is assigned a value ≥0.033 (corresponding to one day).

Note 1: Salt and estuarine waters are define here as those in which the salinity is greater than 1 part per 

thousand 95% or more of the time.

Note 2: When these criteria are used to derive water-quality based effluent limitations for point sources, a 

translator of 1 must be used to convert dissolved selenium criteria values into total recoverable selenium values. 
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 19

4. Method for Estimating Potential Costs: Point Sources

This section describes the method for estimating the potential costs to point sources 

associated with compliance with the revised selenium criteria. Compliance costs for 

municipal and industrial point sources may result from changes to NPDES permit 

requirements and associated effluent limitations.

EPA estimated costs to all potentially affected municipal and industrial dischargers under the 

proposed criteria. This section describes the identification of potentially affected major and 

minor dischargers, reasonable potential analysis (RPA), identification of limits under the 

revised criteria and comparison to existing criteria, and estimation of costs to meet revised 

criteria. Unless otherwise noted, EPA estimated costs in 2015 dollars, and where necessary,

EPA updated cost estimates using the Engineering New Record construction cost index.

4.1 Identification of Potentially Affected Point Source Dischargers

As discussed in Section 3, the proposed selenium criteria are applicable to marine and 

estuarine waters of San Francisco Bay and Delta. Of the point sources permitted to discharge 

to these waters (see Exhibit 2-4), only a small share would need to implement incremental 

controls pursuant to the proposed criteria. Permittees discharging to North San Francisco Bay 

(a majority of the facilities) are subject to the North Bay TMDL adopted by the SFRWQCB. 

EPA anticipates that facilities subject to the TMDL will not incur any compliance costs due 

to the proposed criteria (see Section 2).

EPA also evaluated permittees discharging to the Delta under the jurisdiction of the 

CVRWQCB for applicability under the proposed criteria. Based on a review of the existing 

NPDES permits for permittees in this area, EPA determined that in all instances the 

CVRWQCB had categorized the permittees as freshwater discharges not subject to 

marine/estuarine criteria. Therefore, these permittees were not included in the costing 

population of potentially affected point source dischargers.

Permittees discharging to San Francisco Bay who are not regulated under the North Bay 

TMDL (i.e., dischargers to South Bay which includes all dischargers south of the I-80 

bridge) will be subject to the proposed criteria and potentially subject to incremental control 

costs. Using salinity evaluations conducted by the SFRWQCB and reported in the 

permittees’ existing permits, EPA identified all permittees discharging to these waters 

meeting the salinity condition of the criteria (i.e., marine or estuarine waters). NPDES 

permittees discharging to marine or estuarine waters of the Bay and which are not subject to 

the North Bay TMDL may be affected by the proposed criteria, and EPA included these 

facilities in the cost estimates described below.

Exhibit 4-1 and Exhibit 4-2 provide a summary of the facilities that EPA identified as 

potentially affected by the revised selenium criteria. Appendix A provides additional 

information on these facilities.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 20

Exhibit 4-1. Summary of Potentially Affected Point Source Dischargers

NPDES 

Number Facility Name

Major or 

Minor

Average Dry 

Weather Flow 

(mgd)1

 Municipal Facilities

CA0037621 City of Sunnyvale Major 29.5

CA0037842 City of San Jose/Santa Clara Major 167

CA0037834 City of Palo Alto Major 39

CA0038369 South Bayside System Authority Major 29

CA0037541 City of San Mateo/Foster City Estero Major 15.7

CA0038636 East Bay Regional Park District, Hayward Marsh Major 2.6

CA0037532 City of Millbrae and North Bayside Systems Unit Major 3

CA0037788 City of Burlingame and North Bayside Systems Unit Major 5.5

CA0038130 Cities of South San Francisco, San Bruno, and North 

Bayside Systems Unit Major 13

CA0038008 City of Livermore and EBDA Major 8.5

CA0037613 Dublin San Ramon Services District, LAWMA, and 

EBDA Major 20.2

CA0037869 East Bay Dischargers Authority, Joint Outfall Major 107.8

CA0037664 San Francisco Southeast Plant Major 84.5

CA0038440 East Bay Municipal Utility District, Wet Weather Minor 158

 Industrial Facilities

CA0038318 San Francisco International Airport Major 2.2

CA0030058 Bottling Group, LLC Minor 0.14

mgd = million gallons per day

1. Average dry weather flow from facility NDPES permit fact sheets.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 21

Exhibit 4-2. Locations of Potentially Affected Point Source Dischargers

1. San Francisco Southeast Plant;

2. City of Livermore and EBDA;

Dublin San Ramon Services District, LAWMA, and 

EBDA;

East Bay Dischargers Authority, Joint Outfall;

3. City of Millbrae and North Bayside Systems Unit;

City of Burlingame and North Bayside Systems Unit;

Cities of South San Francisco, San Bruno, and North 

Bayside Systems Unit;

San Francisco International Airport;

4. East Bay Municipal Utility District, Wet Weather;

5. East Bay Regional Park District, Hayward Marsh;

6. City of San Mateo/Foster City Estero;

7. South Bayside System Authority;

8. Bottling Group, LLC;

9. City of Palo Alto;

10. City of San Jose/Santa Clara;

11. City of Sunnyvale;

Note: Permittees who share an outfall pipe, or whose outfall pipes are located in 

close proximity to one another, are displayed as sharing a location.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 22

4.2 Reasonable Potential Analysis

For each facility, EPA conducted an RPA to determine whether there is reasonable potential 

for the effluent to cause or contribute to an excursion above the water quality criteria for 

selenium. EPA based this analysis on procedures established in the SIP for evaluating and 

establishing WQBELs, and on the standard practices utilized at the SFRWQCB. 

EPA conducted RPAs for each facility in the costing population using site-specific effluent 

monitoring data collected from the CIWQS. To best represent current effluent conditions, 

EPA utilized all available data collected on or after September 1, 2010 (i.e., the most recent 

five years of data). Typically, less than five years of data were available, in which case, EPA 

utilized all available data for a facility. If no data were available in CIWQS, EPA performed 

the RPA using data reported in the permittee’s existing permit as of September 1, 2015.

For dischargers to the San Francisco Bay, the SFRWQCB typically evaluates ambient 

background selenium conditions using data collected by a regional monitoring program. 

Using the existing permits, EPA identified the ambient monitoring stations utilized for each 

discharger and collected all available selenium data associated with these stations.

In conformance with the SIP, EPA compared each facility’s maximum effluent concentration 

(MEC) for the period of record and the maximum observed receiving water concentration (B) 

to the proposed selenium dissolved water column criterion of 0.2 μg/L (using a translator of 

1; see Section 4.3). If the MEC exceeds the criterion, then a limitation must be imposed. 

Additionally, if B exceeds the criterion and selenium is present in the discharge in detectable 

amounts, then a limitation must be imposed. The SIP also allows the finding of reasonable 

potential when the permit writer determines that other information indicates a limitation is 

warranted. As such, EPA reviewed the permittees’ existing permits to determine whether any 

of them have reasonable potential pursuant to this provision; however, EPA did not identify 

any such cases, and none of the permittees have reasonable potential under the baseline 

scenario. 

Exhibit 4-3 summarizes the results of the RPA for all potentially affected facilities.

Exhibit 4-3. Summary of Selenium Reasonable Potential Analysis 

NPDES 

Number Facility Name

Max Selenium Conc. (μg/L) RP?5

Effluent1 Background

Baseline

Criteria

Revised

Criterion

Municipal Facilities

CA0037621 City of Sunnyvale 1.66 0.6282 No Yes

CA0037842 City of San Jose/Santa Clara 0.7 0.6282 No Yes

CA0037834 City of Palo Alto 2.6 0.6282 No Yes

CA0038369 South Bayside System 

Authority 0.77 0.393 No Yes
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 23

Exhibit 4-3. Summary of Selenium Reasonable Potential Analysis 

NPDES 

Number Facility Name

Max Selenium Conc. (μg/L) RP?5

Effluent1 Background

Baseline

Criteria

Revised

Criterion

CA0037541 City of San Mateo/Foster City 

Estero 0.536 0.393 No Yes

CA0038636 East Bay Regional Park 

District, Hayward Marsh 0.557 0.393 No Yes

CA0037532 City of Millbrae and North 

Bayside Systems Unit 0.486 0.393 No Yes

CA0037788 City of Burlingame and North 

Bayside Systems Unit 1 0.393 No Yes

CA0038130

Cities of South San Francisco, 

San Bruno, and North Bayside 

Systems Unit

2.7 0.393 No Yes

CA0038008 City of Livermore and EBDA 1.7 0.393 No Yes

CA0037613 Dublin San Ramon Services 

District, LAWMA, and EBDA 4.7 0.393 No Yes

CA0037869 East Bay Dischargers 

Authority, Joint Outfall 1.2 0.393 No Yes

CA0037664 San Francisco Southeast 

Plant 1.26 0.393 No Yes

CA0038440

East Bay Municipal Utility 

District, Wet Weather None; all discharges prohibited

Industrial Facilities

CA0038318 San Francisco International 

Airport 0.1719 0.393 No Yes

CA0030058 Bottling Group, LLC <0.2 2.54 No No

g/L = micrograms per liter

1. California Integrated Water Quality Information System

2. San Francisco Regional Monitoring Program – Monitoring Station BA30 (Dumbarton Bridge)

3. San Francisco Regional Monitoring Program – Monitoring Station BC10 (Yerba Buena Island)

4. Site-specific monitoring data

5. RP = reasonable potential to cause or contribute to an exceedance of a water quality criterion

6. Detected, but Not Quantified (DNQ); i.e., selenium was detected in the sample but at levels too low 

to accurately quantify; the reported concentration is a best estimate as determined by the laboratory 

instrumentation and methodology.

7. No recent data available; effluent data for East Bay Regional Park District, Hayward Marsh, based 

on monitoring data reported in the 2011 NPDES permit.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 24

4.3 Projecting Effluent Limitations

For the 14 facilities that have reasonable potential to cause or contribute to an exceedance 

above the proposed selenium criterion, EPA calculated selenium limitations based on the 

procedures contained in Section 1.4 of the SIP and the proposed criteria. These include an 

accounting of available dilution—as reported in a permittee’s existing NPDES permit—and 

the variability of selenium concentrations in the permittee’s effluent discharge using the 

coefficient of variation. In conformance with the SIP, the effluent selenium data must meet 

certain data quality standards (i.e., at least 10 observations and no more than 80 percent of 

the observations may be non-detect). If these standards were not met, then a coefficient of 

variation of 0.6 was assumed in the calculation of the limits. Otherwise, EPA computed the 

coefficient of variation based on the effluent monitoring data. 

SIP procedures allow for the establishment of mixing zones and dilution credits under certain

circumstances. EPA identified those permittees where the SFRWQCB had established 

mixing zones using the existing NPDES permits. However, dilution credits may only be 

applied in circumstances where assimilative capacity exists in the receiving water to 

incorporate the additional pollutant loading. According to SIP procedures, assimilative 

capacity is considered to be insufficient when the maximum observed receiving water 

observation (B) exceeds the criteria of concern. In this circumstance, B exceeds the proposed 

dissolved water column criterion for all permittees in the costing population as shown in 

Exhibit 4-3. Therefore, EPA did not apply dilution credits for dischargers in the costing 

population.

The following demonstrates how WQBELs based on the proposed criterion were established 

for this analysis. The process for developing these limits is in accordance with Section 1.4 of 

the SIP.

Step 1: For each constituent requiring an effluent limit, identify the applicable water quality 

criterion or objective. For each, determine the effluent concentration allowance (ECA) using 

the following steady state equation:

ECA = C + D (C - B); when C>B, and

ECA = C; when C≤ B,

Where C = The priority pollutant criterion/objective, adjusted if 

necessary for translators. The applicable translator for 

selenium in this instance is 1, so no adjustment is necessary. 

D = The dilution credit, and

B = The ambient background concentration
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 25

For the permittees in the costing population, insufficient assimilative capacity was available 

for dilution (i.e., C≤ B) and, therefore:

ECA = C

For selenium, the applicable proposed water quality criteria are 0.2 μg/L.

Step 2: For each ECA based on aquatic life criterion/objective, determine the long-term 

average discharge condition (LTA) by multiplying the ECA by a multiplier factor. The 

multiplier is a statistically based factor that adjusts the ECA to account for effluent 

variability. The value of the multiplier varies depending on the coefficient of variation of the 

data set and whether it is an acute or chronic criterion/objective. Equations to develop the 

multipliers in place of using values in the tables are provided in Section 1.4, Step 3 of the SIP 

and will not be repeated here.2

LTAacute = ECAacute x Multiplieracute

LTAchronic= ECAchronic x Multiplierchronic

The coefficient of variation for the data set must be determined before the multipliers can be 

selected and will vary depending on the number of samples and the standard deviation of a 

data set. If the data set is less than 10 samples, or at least 80% of the samples in the data set 

are reported as non-detect, the CV shall be set equal to 0.6.

Using the City of Sunnyvale POTW (NPDES No. CA0037621) as an example, the following 

data were used to develop the chronic LTA based on the procedures in section 1.4 Step 3 of 

the SIP:

LTAchronic= ECAchronic x Multiplierchronic = 0.2 μg/L x 0.53 = 0.11 μg/L

In this case, the acute LTA is not applicable

Step 3: Select the most limiting (lowest) of the LTA.

LTA = most limiting of LTAacute or LTAchronic

Since the proposed criteria are chronic, the most limiting LTA is the LTAchronic

LTA = 0.11 μg/L

Step 4: Calculate the WQBELs by multiplying the LTA by a factor (multiplier). WQBELs 

are expressed as Average Monthly Effluent Limitations (AMEL) and Maximum Daily 

Effluent Limitations (MDEL). The multiplier is a statistically based factor that adjusts the 

LTA for the averaging periods and exceedance frequencies of the criteria/objectives and the 

effluent limitations. The value of the multiplier varies depending on the probability basis, the 

coefficient of variation of the data set, the number of samples (for AMEL) and whether it is a 

 

2 The acute ECA multipliers varied from 0.22 to 0.65, and chronic ECA multipliers varied from 0.40 to 0.80.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 26

monthly or daily limit. Equations to develop the multipliers are provided in Section 1.4, 

Step 5 of the SIP and will not be repeated here.3

AMELaquatic life = LTA x AMELmultiplier

MDELaquatic life = LTA x MDELmultiplier

AMEL multipliers are based on a 95th percentile occurrence probability, and the MDEL 

multipliers are based on the 99th percentile occurrence probability. 

Using the City of Sunnyvale POTW as an example, the following data was used to develop 

the AMEL and MDEL for aquatic life:

AMELaquatic life = LTA x AMELmultiplier = 0.11 μg/L x 1.55 = 0.16 μg/L

MDELaquatic life = LTA x MDELmultiplier = 0.11 μg/L x 3.11 = 0.33 μg/L

Step 5: For the ECA based on human health, set the AMEL equal to the ECAhuman health.

However, there are no human health water quality criteria for selenium; therefore, effluent 

limitations based on human health criteria could not be calculated.

Step 6: Select the lower of the AMEL and MDEL based on aquatic life and human health as 

the WQBELs. 

Since there are no applicable human health criteria for selenium, final limitations for each 

facility were based on the AMEL and MDEL associated with the aquatic life criterion.

Exhibit 4-4 summarizes the effluent limitations that EPA calculated for each facility based on

the proposed water column criterion and effluent variability, according to the procedures 

described in the SIP. As the AMEL is the most stringent limitation of the AMEL and MDEL,

and is the relevant limitation used in the control increment analysis, only the AMEL is 

reported in Exhibit 4-4.

Exhibit 4-4. Summary of Selenium Effluent Limitations

NPDES 

Number Facility Name

MEC

(μg/L)

AMEL (μg/L)1

Control 

Baseline Revised Increment

Municipal Facilities

CA0037621 City of Sunnyvale 1.66 -- 0.16 Yes

CA0037842 City of San Jose/Santa Clara 0.7 -- 0.18 Yes

CA0037834 City of Palo Alto 2.6 -- 0.19 Yes

CA0038369 South Bayside System 

Authority

0.77

-- 0.17 Yes

CA0037541 City of San Mateo/Foster City 

Estero

0.532

-- 0.18 Yes

 

3 The MDEL multipliers varied from 1.53 to 4.48, and the AMEL multipliers varied from 1.16 to 1.85.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 27

Exhibit 4-4. Summary of Selenium Effluent Limitations

NPDES 

Number Facility Name

MEC

(μg/L)

AMEL (μg/L)1

Control 

Baseline Revised Increment

CA0038636 East Bay Regional Park 

District, Hayward Marsh

0.55

-- 0.16 Yes

CA0037532 City of Millbrae and North 

Bayside Systems Unit

0.482

-- 0.16 Yes

CA0037788 City of Burlingame and North 

Bayside Systems Unit

1.0

-- 0.17 Yes

CA0038130

Cities of South San 

Francisco, San Bruno, and 

North Bayside Systems Unit

2.7

-- 0.17 Yes

CA0038008 City of Livermore and EBDA 1.7 -- 0.16 Yes

CA0037613 Dublin San Ramon Services 

District, LAWMA, and EBDA

4.7

-- 0.15 Yes

CA0037869 East Bay Dischargers 

Authority, Joint Outfall

1.2

-- 0.17 Yes

CA0037664 San Francisco Southeast 

Plant

1.17

-- 0.16 Yes

CA0038440

East Bay Municipal Utility 

District, Wet Weather

--

-- -- No

Industrial Facilities

CA0038318 San Francisco International 

Airport

0.17

-- 0.16 Yes

CA0030058 Bottling Group, LLC <0.2 -- -- No

AMEL = average monthly effluent limitation

MEC = maximum effluent concentration

μg/L = micrograms per liter

1. The AMEL is the most stringent (i.e., lowest in magnitude) effluent limitation and is the controlling 

limitation in the cost analysis.

2. Detected, but Not Quantified (DNQ); i.e., selenium was detected in the sample but at levels too low 

to accurately quantify; the reported concentration is a best estimate as determined by the laboratory 

instrumentation and methodology.

Minimum levels to be used by permittees when assessing compliance with effluent 

limitations have been specified in Appendix 4 of the SIP. A minimum level is the lowest 

quantifiable concentration in a sample based on the proper application of all method-based 

analytical procedures and the absence of any matrix interferences. The minimum level is also 

sometimes referred to as the limit of quantitation or the reporting level. 

The SIP requires that, when assessing a parameter with an effluent limitation, the permittee 

must use an analytical method with an approved minimum level below the limitation or—if 

none satisfy the previous condition—the lowest approved minimum level. The SIP specifies 
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 28

six analytical-method-specific minimum levels for selenium, the lowest of which is 1 μg/L 

using gaseous hydride atomic absorption. Compliance with effluent limitations at 

concentrations below the lowest minimum level cannot be ascertained for those permittees 

currently discharging at detectable levels below the minimum level (i.e., the MEC is less than 

1 μg/L). For example, standard language in the Monitoring and Reporting Program section 

VIII.B.5 for Order R2-2014-0024 for the City of Palo Alto (NPDES No. CA0037834) states 

that “the Discharger shall be deemed out of compliance with effluent limitations if the 

concentration of the priority pollutant in the monitoring sample is greater than the effluent 

limitation and greater than or equal to the [minimum level].” 

4.4 Compliance Scenarios and Costs

EPA calculated compliance costs for all dischargers for which a selenium control increment 

may be needed. As discussed in Section 4.2, 14 point source dischargers may require

additional compliance actions in order to comply with the proposed water column criterion. 

EPA developed likely compliance scenarios and associated incremental costs for each 

permittee. For a permittee-by-permittee discussion of likely compliance scenarios and 

associated costs, refer to Appendix A.

4.4.1 Potential Compliance Scenarios

There are a number of potential alternatives for compliance with effluent limits for selenium, 

including: 

 Optimizing treatment processes (e.g., adding chemicals to increase flocculation or 

filtration efficiency) to increase pollutant removal efficiencies;

 Source control (e.g., pollution prevention program, inflow and infiltration reductions, 

more stringent pretreatment standards);

 Installing end-of-pipe treatment technology (e.g., reverse osmosis (RO), or chemical 

precipitation); or

 Alternative compliance mechanisms (e.g., site-specific criteria, dilution credits, TMDL, 

or variance).

In addition to the above compliance alternatives, the Regional Water Boards may establish 

compliance schedules for permittees. A compliance schedule provides a discharger with a 

specific period of time to plan and implement compliance alternatives. A permittee who 

seeks a compliance schedule must demonstrate to the satisfaction of the Regional Water 

Board that time is needed to implement actions, such as designing and constructing facilities 

or implementing new or significantly expanded programs and securing financing, if 

necessary, to comply with a more stringent permit limitation specified to implement a new or 

revised water quality criteria. 

Process Optimization

The lowest cost option is likely the adjustment of existing treatment (process optimization).

This option would be most feasible when relatively low pollutant reductions are needed.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 29

Process optimization usually involves process analysis and process modifications. Process 

analysis is an investigation of the performance-limiting factors of the treatment process and 

is a key factor in achieving optimum treatment efficiency. Performance-limiting factors for 

common wastewater treatment processes (e.g., sedimentation, activated sludge, filtration) 

may include operator training, response to changes in wastewater quality, maintenance 

activities, automation, and process control testing. The cost of process analysis includes the 

cost of additional monitoring throughout the treatment process, and a treatment performance 

evaluation which encompasses jar testing and an operations analysis.

Process modifications include activities short of adding new treatment technology units 

(conventional or unconventional) to the treatment train. For increasing pollutant removal 

efficiencies, process modifications could include adjusting coagulant doses to increase 

settling, equalizing flow if pollutant concentrations spike during wet weather events, 

increasing filter maintenance activities or backwash cycles, training operators, and installing 

automation equipment including necessary hardware and software. Several months of 

adjustments may be needed to achieve a desired level of process optimization. In practice, the 

process modifications necessary would be determined by the process analysis study.

Process optimization costs depend on the characteristics of the wastewater being treated and 

existing unit process and operations. For example, a facility could alter the type or dose of a 

flocculent aid to increase solids removal, and thus, the removal of selenite adhered to 

particulates. Or, to the extent practicable, hydraulic residence times could be extended or 

shortened to produce more favorable treatment outcomes. 

The effectiveness of process optimization largely depends on the efficiency of current 

operations and the types of existing unit processes within the treatment plant. For example, if 

a facility is already well maintained and operated, implementing process optimization may 

not result in sufficient incremental selenium removals because the existing treatment 

processes are already performing at the limits of technical feasibility. Given the available 

information for the sample facilities, it is generally not possible to determine the reductions 

achievable with process optimization; rather, a detailed, site-specific study would be 

necessary.

EPA developed an estimate of the cost necessary to complete a typical process optimization 

study. This cost estimate assumes 48 wastewater samples will be collected by a POTW 

operator and analyzed at an off-site laboratory, approximately 20 jar tests will be run in order 

to assess the effect of varying chemical doses and reaction times, and a process engineer will 

synthesize the resulting information and develop recommendations for implementing process 

changes (see Exhibit 4-5). EPA developed costs based on May 2014 Bureau of Labor 

Statistics mean hourly wage data4for a California POTW operator and California 

 

4 http://www.bls.gov/oes/current/oes_ca.htm; retrieved November 3, 2015.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 30

Environmental Engineer, and publicly available pricing data for laboratory analyses.

5 Due to 

the site-specific nature of any process optimization plan, EPA is unable to estimate costs for 

implementing plant operational changes.

Exhibit 4-5. Summary of Process Optimization Study

Activity Component No. of Units Unit Cost1 Sub-Total

Sampling

POTW Operator 48 samples $31.93 $1,533

Lab Costs 48 samples $40.00 $1,920

Jar Testing

POTW Operator 20 jar tests $31.93 $639

Lab Costs 20 jar tests $40.00 $800

Engineering 

Analysis

Environmental 

Engineer 320 person hours $144.802 $46,945

Total $51,836

1. Costs are presented in 2015 dollars.

2. Mean wage has been multiplied by 3.03 to account for overhead, administrative costs, and profit.

Source Controls

The population of permittees that is likely to be subject to selenium control increments is 

composed of POTWs and the San Francisco International Airport wastewater treatment plant

(WWTP). Insufficient information is available to conclusively identify the sources of 

selenium in these discharges; however, evidence suggests the source could be unusually high 

levels of selenium present in drinking water sources and ground water sources. A literature 

review by Anderson (1998) reported high levels of naturally occurring selenium present in 

bedrock units, soils, ground water, and municipal drinking water supplies in the South San 

Francisco Bay region. 

If the pollutant source is traced back to drinking water sources and municipal service supply, 

it is unlikely that the control increment could be addressed through source control measures

since the maximum contaminant level for selenium in these sources is 50 μg/L. Note that the 

maximum contaminant level applicable to drinking water sources is substantially greater than 

either the existing water quality chronic criterion (5 μg/L) or proposed criterion (0.2 μg/L) 

for the protection of aquatic life and aquatic-dependent wildlife. Addressing contamination 

through source control activities would necessitate either shifting the locus of control to 

drinking water treatment plants, which would present regulatory challenges and likely result 

in equivalent control costs; or changing the source of drinking water, which might not be 

technically feasible and could be cost prohibitive. 

Should the source of selenium be traced to industrial activities, a pollution prevention 

program or other source control activities may be productively employed to control selenium. 

 

5 http://www.wtlmd.com/wastewater-testing-pricing-maryland-md-va-dc-de.php; retrieved November 3, 2015.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 31

Common industrial sources of selenium include petroleum refineries, steam-electric 

generating stations, metals manufacturing, coal mining, and other resource extraction and 

processing industries (EPA, 1983). In order to identify any industrial discharges to the 

POTWs, EPA reviewed the existing Fact Sheets for each of the dischargers. The documents 

did not report any industrial discharges which could be contributing to selenium levels in the 

POTW discharges. Because available information suggests that, in these cases, industrial 

sources are unlikely to be a significant source of selenium to the POTWs , EPA has assumed 

that source control activities are unlikely to be successfully deployed for selenium control at 

facilities within the costing population.

End-of-Pipe Treatment

If process optimization or source control would not be sufficient for compliance with the 

revised criterion, alternative discharge options or end-of-pipe treatment technologies may be 

necessary. However, the proposed criterion approaches the limits of analytical capabilities 

and falls below California’s most stringent required quantification level (QL) for selenium 

(i.e., 1 μg/L). In addition, the lowest levels achievable through end-of-pipe treatment are 

highly uncertain due to the fact that dischargers in the United States have not previously been 

required to treat to such low levels and a demonstrable technical capability to comply with 

the proposed selenium criterion is not available.

In municipal and industrial wastewaters, selenium occurs in a variety of chemical forms and 

oxidation states. The various forms of selenium vary in their amenability to removal based on 

the technology employed—for instance, selenite is much more amenable to iron coprecipitation treatment than selenate. Consequently, successful end-of-pipe treatment control 

depends on how selenium is speciated within a given facility’s waste stream.

Selenite—the reduced form of selenium—is amenable to removal by conventional chemical 

treatment technologies. The effectiveness of these technologies can be enhanced when paired 

with the addition of an iron salt. The addition of iron can, under certain pH conditions, 

encourage the formation of precipitates which are relatively insoluble, readily removable, 

and adsorb selenite to their surfaces. Chemical precipitation of selenite as part of a 

coagulation and filtration process is currently among EPA’s Best Available Technologies for 

selenium removal in water treatment plants.

Selenate, however, is largely resistant to conventional chemical precipitation techniques. 

Selenate can be removed via ion exchange resins, though the effectiveness of this application 

is inhibited by the presence of phosphates—a common constituent of municipal wastewaters. 

Alternatively, selenate can be reduced to the more readily removable selenite through 

chemical (i.e., addition of elemental iron) or biological means. Both reduction processes will 

be hindered by the presence of sulfates or nitrates. Data on the presence of nitrates and 

sulfates are not available for most Bay area plants; however, most of these facilities are 

required to comply with stringent ammonia water quality criteria and, consequently, it is very 

likely that nitrates are present at high levels in most treatment plant effluents.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 32

Biological reduction of selenate is an application of biological treatment processes and has 

been implemented at relatively small scales at various industrial facilities around the United 

States over the past 10 to 20 years. Typically, this involves the construction of a biofilter, 

slow sand denitrification filter, or anoxic tank. In principle, the same biological treatment 

processes utilized in municipal WWTPs to remove nitrates could be used to reduce selenate 

to selenite, rendering it amenable to removal using chemical precipitation with iron salts. 

However, since nitrates are likely to be present in large quantities in the municipal 

wastewaters and because nitrates inhibit selenate reduction, full nitrogen removal would 

likely be necessary in order to encourage selenate reduction in a POTW treatment train.

Another treatment option would be use of RO to remove all selenium species. Similar to the 

other technologies discussed herein, selenium treatability below the proposed criterion has 

not been definitively demonstrated. However, successful control using RO is likely, due to 

RO’s ability to remove nearly all ions from treated water, including selenium species. 

However, due to the scale of implementation that would be required, EPA assumes it is 

unlikely municipal WWTPs would ultimately utilize this technology due to its prohibitive 

expense. 

Exhibit 4-6 summarizes the end-of-pipe treatment technologies that may be used to remove 

selenium. 

Exhibit 4-6. Summary of Potential End-of-Pipe Treatment Technologies

Technology Pollutants Removed

Chemical precipitation with iron salts Selenite removed

Biological reduction Selenate transformed to selenite

Reverse osmosis All selenium species removed

For this analysis, and as documented in the facility analyses in Appendix A, EPA assumed 

that permittees requiring end-of-pipe treatment to meet selenium limitations will utilize 

chemical precipitation with iron salts paired with sand filtration. Given the limited treatment 

data testing using analytical methods at or below the proposed criterion, and the uncertainty 

regarding the selenium speciation within the wastewaters, EPA has assumed the use of

conventional treatment technologies (i.e., chemical precipitation and filtration) to achieve 

compliance. Chemical precipitation paired with filtration is a widely adopted technology 

which has been demonstrated to achieve low effluent concentrations (i.e., less than 1 μg/L; 

EPA, 1983).

EPA was unable to identify studies which have documented treatment capabilities for any 

treatment technology at the levels of the proposed water column criterion (i.e., 0.2 μg/L) or 

the estimated effluent limitations, as most studies utilize analytical methods with detection 

levels well in excess of the criterion. Therefore, EPA cannot state with certainty that the 

proposed treatment alternatives will result in compliance with effluent limitations in all 
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 33

cases, as the existing literature has not heretofore utilized analytical methods of sufficient 

sensitivity to detect the pollutant at these concentrations. 

However, EPA has identified data (EPA, 1983; Kapoor, et al., 2007) which document 

effluent treatment levels for chemical treatment methods at levels equal to or below the 

minimum quantification level required under California’s adopted implementation 

procedures (i.e., 1 μg/L) without sand filtration. By pairing this performance with sand 

filtration, there is a reasonable likelihood that effluent treatment consistent with the proposed 

criterion may be achievable.

Utilizing facility descriptions and treatment process flow diagrams enclosed in the existing 

permits, EPA evaluated whether each of the following unit operations were present for each 

facility: iron salt coagulation and flocculation, and sand filtration. If one or both of the items 

were not present, EPA estimated costs to install the process. 

EPA developed cost curves fitted to costs developed for four model treatment trains: 1 mgd, 

10 mgd, 100 mgd, and 200 mgd. Costs for each treatment train were developed as follows. 

For coagulation flocculation costs, costs were developed on the basis of installing a ferric 

sulfate feed system and chemicals, a polymer feed system and chemicals, a rapid mixer, a 

flocculation basin, and a tertiary clarifier. Capital costs, and operations and maintenance 

costs (O&M) were developed for each unit process using cost curves developed by EPA 

(1979). Costs for sand filters included down flow filter and media costs and were based on 

cost estimates developed using CapdetWorksTM construction cost estimating software. 

Capital and O&M costs were escalated to 2015 dollars using the Engineering News Record 

construction cost index. Using the resultant cost curves for coagulation/flocculation and for 

media filtration, EPA estimated costs for each permittee.

EPA assumed the indirect costs listed in Exhibit 4-7 in all construction cost estimates. Cost 

curves are presented in Exhibit 4-8.

Exhibit 4-7. Summary of Potential End-of-Pipe Treatment Technologies

Indirect Cost Percentage of Direct Capital Costs

Mobilization 6%

Site Preparation 7%

Site Electrical 16%

Yard Piping 11%

Instrumentation and Control 8%

Legal Costs 2%

Engineering Design Fee 15%

Inspection Cost 2%

Contingency 15%

Profit 15%
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 34

Exhibit 4-8. Summary of Potential End-of-Pipe Treatment Unit Cost Curves1

Treatment Addition Capital Costs O&M Costs

Chemical Treatment $1,922,907 + $284,871/mgd x Q $63,681 + $7,771/mgd x Q 

Sand Filtration $1,661,321 + $189,620/mgd x Q $100,945 + $9,872/mgd x Q 

Chemical Treatment and 

Sand Filtration $3,584,229 + $474,491/mgd x Q $164,627 + $17,643/mgd x Q 

Q = System flow capacity in million gallons per day (mgd).

1. All costs are reported in 2015 dollars. Capital costs include both direct and indirect costs.

Given the uncertainties surrounding the capability of achieving effluent compliance 

with conventional treatment technologies, EPA has performed a sensitivity analysis 

of this cost estimate. For additional details on this analysis, refer to Section 6.

Alternative Compliance Mechanisms

If none of the control options discussed above would result in compliance with effluent 

limitations, or if the costs would be prohibitive, dischargers would likely need some form of 

relief from the requirements.

Site-Specific Criteria

If dischargers suspect that the conditions in the vicinity of their discharge warrant alternative 

(i.e., site-specific) criteria values that would result in less stringent effluent limitations in 

their permit, they may work to collect data to develop site-specific criteria. The Water Board 

may also develop site-specific criteria as part of a TMDL process (i.e., identifying the 

appropriate target value). EPA must review and approve site-specific criteria prior to 

implementation.

Because additional data are required to assess the appropriateness of site-specific criteria at a 

particular location, the extent of use of this mechanism by dischargers is uncertain. However, 

consideration within the context of a TMDL is likely, and may or may not reflect an 

incremental increase in effort above that associated with current TMDLs (this type of data 

collection and evaluation may already be a part of TMDL development efforts).

Intake Credits

Under California’s WQS implementation provisions, Water Boards may establish intake 

credits for intake water taken from municipal supply, or intake water that is taken from and 

discharged to the same waterbody. EPA has insufficient information at this time to evaluate 

the sources of selenium in the permittees’ influents. In addition, it is unclear whether 

selenium sources which may originate from groundwater or domestic supply and used 

municipally would qualify for credits under this provision. Therefore, EPA has 

conservatively assumed that intake credits are unlikely to serve as a valid compliance action 

for the proposed selenium criterion. 
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 35

Dilution Credits

Under California’s WQS implementation provisions, Water Boards may implement mixing 

zones and associated dilution credits in NPDES permits. As discussed above, EPA evaluated 

currently implemented mixing zones when calculating WQBELs for the facilities. Due to the 

lack of available assimilative capacity in the receiving waters, EPA assumed that dilution 

credits are an unlikely compliance approach.

4.4.2 Summary of Facility Control Costs

For plants discharging at levels above the QL, EPA assumed that they will pursue 

conventional treatment methods to comply with the projected effluent limitations. EPA based 

unit costs for end-of-pipe treatment on cost curves previously developed by EPA (1979), unit

process costs estimated using CapdetWorksTM cost estimating software, and indirect cost 

assumptions. EPA updated these costs to reflect local labor rates and escalated to 2015 

dollars using the Engineering News Record Construction Cost Index.

Facilities operating below the QL are discharging near the projected limitations and EPA has 

assumed that compliance is likely to be achievable using process optimization methods. EPA 

developed costs associated with process optimization special studies as described in Section 

4.4.1.

To calculate annual costs for the main analysis, EPA discounted all one-time and capital 

costs over 20 years using a 3 percent discount rate. Results using a 7 percent discount rate are 

provided in Appendix B.

Exhibit 4-9 summarizes the unit costs utilized in the sample facility compliance cost 

analyses.

Exhibit 4-9. Estimated Unit Costs of Compliance Mechanisms (2015$)

Compliance 

Mechanism One-Time Cost Estimate O&M Cost Estimate

Process Optimization $52,000 --

Chemical Treatment $1,922,907 + $284,871/mgd x Q $63,681 + $7,771/mgd x Q 

Sand Filtration $1,661,321 + $189,620/mgd x Q $100,945 + $9,872/mgd x Q 

Chemical Treatment 

and Sand Filtration $3,584,229 + $474,491/mgd x Q $164,627 + $17,643/mgd x Q 

Q = Plant capacity in million gallons per day (mgd).

Exhibit 4-10 summarizes the one-time (capital or process optimization) costs, O&M costs, 

and total annual cost for each of the identified facilities likely to have a control increment 

under the proposed selenium criterion. See Appendix A for facility-specific descriptions of 

the cost estimates.
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 36

Exhibit 4-10. Treatment and Estimated Cost Increment for Affected Facilities1

NPDES 

Number Facility Name Capacity (mgd)

MEC 

(μg/L)

AMEL 

(μg/L)

One-Time

Cost O&M Cost Total Annual Cost2

 Municipal Facilities

CA0037621 City of Sunnyvale 29.5 1.66 0.16 $10,327,000 $293,000 $987,000

CA0037842 City of San Jose/Santa Clara 167 0.7 0.18 $52,000 -- $3,500

CA0037834 City of Palo Alto 39 2.6 0.19 $13,033,000 $367,000 $1,243,000

CA0038369 South Bayside System Authority 29 0.77 0.17 $52,000 -- $3,500

CA0037541 City of San Mateo/Foster City Estero 15.7 0.533 0.18 $52,000 -- $3,500

CA0038636 East Bay Regional Park District, 

Hayward Marsh 2.6 0.55 0.16 $52,000 -- $3,500

CA0037532 City of Millbrae and North Bayside 

Systems Unit 3 0.483 0.16 $52,000 -- $3,500

CA0037788 City of Burlingame and North Bayside 

Systems Unit 5.5 1 0.17 $6,194,000 $262,000 $678,000

CA0038130 Cities of South San Francisco, San 

Bruno, and North Bayside Systems Unit 13 2.7 0.17 $4,126,000 $229,000 $506,000

CA0038008 City of Livermore and EBDA 8.5 1.7 0.16 $7,617,000 $315,000 $827,000

CA0037613 Dublin San Ramon Services District, 

LAWMA, and EBDA 20.2 4.7 0.15 $13,169,000 $521,000 $1,406,000

CA0037869 East Bay Dischargers Authority, Joint 

Outfall 107.8 1.2 0.17 $54,734,000 $2,067,000 $5,746,000

CA0037664 San Francisco Southeast Plant 84.5 1.23 0.16 $43,679,000 $1,655,000 $4,591,000

CA0038440 East Bay Municipal Utility District, Wet 

Weather 158 -- -- $0 $0 $0

Subtotal $153,139,000 $5,709,000 $16,001,500

 Industrial Facilities

CA0038318 San Francisco International Airport 2.2 0.1719 0.16 $52,000 -- $3,500

Subtotal $52,000 -- $3,500

Total $153,191,000 $5,709,000 $16,005,000
POINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 37

Exhibit 4-10. Treatment and Estimated Cost Increment for Affected Facilities1

NPDES 

Number Facility Name Capacity (mgd)

MEC 

(μg/L)

AMEL 

(μg/L)

One-Time

Cost O&M Cost Total Annual Cost2

mgd = million gallons per day

μg/L = micrograms per liter

1. For plants discharging at levels above the most stringent quantitation level (1 μg/L), EPA assumed that facilities will pursue conventional 

treatment methods to comply with the projected effluent limitations. Facilities operating below the quantitation level are discharging near the 

projected limitations and EPA has assumed that compliance is likely to be achievable using process optimization methods.

2. One-time costs annualized over 20 years using a 3 percent discount rate; for costs annualized using a 7 percent discount rate, see Appendix B.

3. Detected, but Not Quantified (DNQ); i.e., selenium was detected in the sample but at levels too low to accurately quantify; the reported 

concentration is a best estimate as determined by the laboratory instrumentation and methodology.
NONPOINT SOURCE COSTS: METHODS

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 38

5. Methods for Identifying Potential Costs: Nonpoint Sources

Unlike point sources, California typically does not require nonpoint sources and municipal 

stormwater dischargers to achieve numeric WQBELs. The regulatory baseline for evaluating 

the potential impact of the revised criteria includes some requirements for nonpoint sources 

and stormwater dischargers to implement BMPs and wasteload allocations as part of TMDLs 

(see Section 2). The CVRWQCB and SFRWQCB have already developed TMDLs for 

selenium in the Lower San Joaquin River and the North Bay, and EPA assumes that the 

proposed selenium criteria will not result in the need for additional controls by nonpoint 

sources in those areas. 

The San Francisco Estuary Project, a federal-state-local partnership established in 1987 under 

the National Estuary Program, is responsible for developing and implementing a 

Comprehensive Conservation and Management Plan (CCMP). According to the 2007 CCMP 

Update (San Francisco Estuary Project 2007), and as it relates to controlling nonpoint sources 

of selenium to the Bay:

“The control strategy should include management practices and waste discharge 

requirements as necessary to limit selenium in agricultural subsurface drainage to 

reduce selenium loadings to the Delta and attain water quality objectives for selenium in 

the San Joaquin River.”

The SFRWQCB has begun developing a TMDL for selenium for the South San Francisco 

Bay. It is uncertain as to the extent nonpoint sources contribute to the overall selenium 

loading to the South Bay, and, as described in Section 2.3.1, naturally-occurring selenium 

may be the primary source of selenium loadings to the South Bay. Although the extent of 

incremental controls that could be required under the potential revised criteria for selenium is 

uncertain, it is expected to be insignificant.
REFERENCES

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 39

6. Summary of Results, Uncertainties, and Quality Assurance

This section summarizes the potential costs to point sources and nonpoint sources, and 

discusses the limitations and uncertainties associated with the analyses.

6.1 Point Sources

Incremental costs associated with the proposed dissolved selenium criterion represent the 

costs of any additional actions or controls needed for compliance with revised WQBELs 

under the proposed rule, beyond the actions or controls needed to meet the existing criteria 

under the baseline.

6 For compliance with revised WQBELs under the proposed rule, for the 

51 dischargers within the confines of San Francisco Bay and Delta, EPA estimates the total 

annual social cost to be approximately $16 million across 14 facilities. Of these costs, nearly 

all are attributable to municipal dischargers.

6.2 Nonpoint Sources

Potential costs for compliance with the proposed criterion include costs to nonpoint sources 

(e.g., agricultural and forest operations; contamination from historic mining sites), and 

municipal stormwater sources associated with implementation of existing programs and 

TMDLs. Incremental costs associated with compliance with the proposed revised criteria

represent the costs of any actions or controls above and beyond those needed to meet 

baseline requirements. The CVRWQCB and SFRWQCB have already developed TMDLs for 

selenium in the North Bay and in the Lower San Joaquin River which flows into the Delta in 

order to control the primary nonpoint sources of selenium to the Delta and northern parts of 

the Bay. Therefore, as discussed in Section 5, additional measures to control the secondary 

nonpoint sources of selenium are unlikely to be necessary. However, if nonpoint sources in 

the South San Francisco Bay are found to be a significant source of selenium, controls could 

include the development and implementation of TMDLs for that part of the Bay. 

6.3 Sensitivity Analysis, Sources of Uncertainty, and Quality Assurance

The proposed rule does not establish any requirements directly applicable to regulated 

entities or other sources of pollution. State implementation of the proposed rule may result in 

new or revised NPDES permit conditions for point source dischargers, and incremental 

control requirements for nonpoint sources. For point sources, EPA has estimated facility-

 

6 Since the effluent data used by EPA to determine reasonable potential, effluent limitations, and compliance 

actions and costs may be more recent than the effluent data used to develop the existing permits, there may 

be some cases where EPA’s analysis indicates some requirements and costs for a facility under the baseline 

scenario that are not reflected in the existing permit for the facility. Such costs would not be attributable to 

the proposed revised criteria, but rather would be baseline costs attributable to the existing criteria. 

However, in this analysis, there are no such baseline costs, and all costs estimated by EPA represent 

incremental costs attributable to the proposed revised criteria.
REFERENCES

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 40

specific costs to reach compliance with the proposed dissolved water column criterion. 

However, there is substantial uncertainty associated with actual state implementation of the 

proposed rule. 

In addition, the existing body of selenium treatment performance data was developed using 

analytical methods that exceed the level of the criterion. As with other economic analyses of 

proposed WQS rules, EPA assumes that facilities will deploy mechanisms to achieve the 

greater of permit limit or the level of detection. This introduces a level of uncertainty into the 

technological achievability of the proposed selenium criterion using existing technologies. 

Given this, EPA has performed a supplementary sensitivity analysis of the end-of-pipe 

treatment costs. If applicable analytical detection limits should come to reach a level 

comparable to projected effluent limits, then it is possible that costs would increase. In the 

case of selenium, EPA has a means to evaluate this contingency. As discussed in Section 4.4, 

the POTW effluent selenium load is composed of multiple selenium species. Two of the most 

abundant are selenite and selenate. The proposed conventional end-of-pipe treatment 

technologies are effective at removing selenite, but are less effective at removing selenate.

Limited data are available on selenium speciation within municipal WWTPs within the San 

Francisco Bay region. A Bay area study dating to the 1980’s (Cutter and San DiegoMcGlone, 1990) indicated that post-treatment municipal effluent was composed of 70 to 90 

percent selenate with the remainder primarily composed of selenite. A similar 2011-2012 

study (Yee, 2012) found that selenium species partitioning was variable from plant-to-plant. 

However, for most plants, selenate was the dominant effluent, followed by organic selenium 

species and selenite.

This sensitivity analysis assumes that all plants requiring end-of-pipe treatment will need to 

install denitrification filters in addition to the previously proposed coagulation/filtration 

units. Denitrification filters will be used to create reducing conditions which will encourage 

the transformation of selenate to selenite. In order to reduce selenate, the denitrification 

filters must first remove a large fraction of any nitrates in the wastestream—resulting in 

partial nitrogen removal as a potential secondary benefit of the approach. By converting 

selenate to selenite, a greater fraction of the selenium load is rendered amenable to 

conventional treatment and is likely to achieve a commensurate improvement in treatment 

performance. 

EPA estimated direct costs for denitrification filters based on the capital ($0.91/gallons per 

day (gpd)) and O&M ($0.064/gpd) unit costs for installing a denitrification filter retrofit to a 

10 mgd plant (EPA, 2008; unit costs are reported in 2015 dollars). This unit capital cost was 

developed with CapdetWorksTM software and represents the total installed cost (i.e., indirect 

costs are included); however, the reference includes neither a total, nor a component 

breakdown of the indirect costs used. Therefore, EPA has assumed that the indirect costs 

used are approximately comparable to those used in EPA’s cost analysis (see Section 4.4). 

Using the resulting flow-normalized unit cost, EPA extrapolated costs for the permittees on 

the basis of each permittee’s flow rate. Due to expected returns to scale, these unit costs are 
REFERENCES

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 41

likely to result in conservative estimates since most plants requiring end-of-pipe treatment 

have capacities greater than 10 mgd.

Exhibit 6-1 summarizes the results of the sensitivity analysis.

Exhibit 6-1. End-of-Pipe Treatment Costs Sensitivity Analysis

NPDES 

Number Facility Name

Total Annual Cost1

Original2

Including 

Denitrification Filter

 Municipal Facilities

CA0037621 City of Sunnyvale $987,000 $4,692,000

CA0037842 City of San Jose/Santa Clara3 $3,500 $3,500

CA0037834 City of Palo Alto $1,243,000 $6,141,000

CA0038369 South Bayside System Authority3 $3,500 $3,500

CA0037541 City of San Mateo/Foster City Estero3 $3,500 $3,500

CA0038636 East Bay Regional Park District, Hayward 

Marsh3

$3,500 $3,500

CA0037532 City of Millbrae and North Bayside Systems 

Unit3

$3,500 $3,500

CA0037788 City of Burlingame and North Bayside 

Systems Unit $678,000 $1,369,000

CA0038130 Cities of South San Francisco, San Bruno, 

and North Bayside Systems Unit $506,000 $2,139,000

CA0038008 City of Livermore and EBDA $827,000 $1,895,000

CA0037613 Dublin San Ramon Services District, 

LAWMA, and EBDA $1,406,000 $3,943,000

CA0037869 East Bay Dischargers Authority, Joint 

Outfall $5,746,000 $19,285,000

CA0037664 San Francisco Southeast Plant $4,591,000 $15,204,000

CA0038440

East Bay Municipal Utility District, Wet 

Weather $0 $0

Subtotal $16,001,500 $54,685,500

 Industrial Facilities

CA0038318 San Francisco International Airport3 $3,500 $3,500

Subtotal $3,500 $3,500

Total $16,005,000 $54,689,000

1. One-time costs annualized over 20 years using a 3 percent discount rate; for costs annualized 

using a 7 percent discount rate, see Appendix B.

2. For plants discharging at levels above the most stringent quantitation level (1 μg/L), EPA assumed 

that facilities will pursue conventional treatment methods to comply with the projected effluent 

limitations. Facilities operating below the quantitation level are discharging near the projected 

limitations and EPA has assumed that compliance is likely to be achievable using process 

optimization methods.

3. End-of-pipe treatment (including denitrification filter) is unnecessary for this facility, even 

considering alternative analytical detection limits.
REFERENCES

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 42

The above analysis evaluates the sensitivity of the cost estimate to assumptions regarding the 

dissolved selenium speciation within the influent of each plant. It shows that making a 

substantially more conservative assumption regarding selenium speciation (i.e., the selenate 

fraction within the influent is significant) still results in cost estimate results which are on the 

same order of magnitude.

Exhibit 6-2 summarizes additional uncertainties and limitations in the analysis.

Exhibit 6-2. Uncertainties in Analysis of Costs

Uncertainty/Assumption

Effects on 

Cost Estimate Notes

Effluent limitations based 

on the proposed criteria 

cannot be met via source 

control

Overestimate

Assumption could result in an overestimate depending 

on the nature of the selenium source (i.e., selenium 

can be diverted from certain waste streams), or it may 

result in transferring the cost of treatment from the 

municipal dischargers to indirect industrial 

dischargers. 

Control increment cannot 

be met via intake credits Overestimate

Should additional data and information indicate intake 

credits are a viable regulatory pathway to meeting the 

control increment for municipal dischargers, EPA 

expects costs would decrease substantially for those 

permittees able to qualify for credits.

Assumed no compliance 

schedules will be used Overestimate

Facilities subject to the proposed criteria requiring 

additional treatment could be provided with 

compliance schedules by the Regional Water Boards. 

A compliance schedule would provide an extended 

period (i.e., ten years) within which a permittee may 

pursue compliance without being subject to penalties 

for exceedances of the limitation. A compliance 

schedule would provide permittees with additional time 

to research and develop more cost-effective treatment 

alternatives than are currently available.

Assumed current South 

Bay urban stormwater 

controls are adequate, 

consistent with the

analysis contained in the 

North Bay TMDL

Underestimate

It is possible that urban non-point sources in the South 

Bay are of a different character from other sources in 

the region (i.e., urban nonpoint sources in the North 

Bay) with respect to selenium, and could require 

incremental control measures and a TMDL.

In order to mitigate sources of uncertainty in the analysis, EPA conducted quality assurance 

checks on the data, analyses, and results, consistent with the programmatic and projectspecific quality assurance plans. In addition, EPA used California-based permit-writing tools 

to ensure consistency with state permitting approaches and calculations. EPA also used 

California-specific data sources as available, and for all data entry, EPA confirmed the 

accuracy of data sources and documentation following procedures described in the quality 

assurance plans. These procedures include checks on all inputs and calculations, and using 

multiple approaches to confirm results.
REFERENCES

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 43

7. References

Anderson, D.W. 1998. Natural levels of nickel, selenium, and arsenic in the southern San 

Francisco Bay area. Prepared for the City of San Jose, Environmental Services Department.

Boerngen, J.G.; Shacklette, H.T. 1981. Chemical analysis of soils and other surficial 

materials of the conterminous United States: U.S. Geological Survey Open-File Report 81-

197.

Cutter, G.A.; San Diego-McGlone M.L.C. 1990. Temporal variability of selenium fluxes in 

San Francisco Bay. Science of the Total Environment 97/98: 235-250.

Central Valley Regional Water Quality Control Board (CVRWQCB) 2001. Total Maximum 

Daily Load for Selenium in the Lower San Joaquin River. Retrieved November 2015 from: 

<http://www.waterboards.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/ind

ex.shtml>

Kapoor, A.; Tanjore, S.; Viraraghavan, T. 2007. Removal of selenium from water and 

wastewater. International Journal of Environmental Studies, 49:2, 137-147, DOI: 

10.1080/00207239508711016.

Kleinfelder, Inc. 1995. Level II hazardous materials investigation upper Guadalupe River 

flood control project: Final Report to the Santa Clara Valley Water District. Retrieved 

November 2015 from: <http://www.valleywater.org/programs/construction.aspx>

Scott, C.M. 1995. Background metal concentrations in soils in northern Santa Clara County, 

California, in Sangines, E.M.; Anderson, D.W.; and Buising, A.V.; eds. Recent geologic 

studies in the San Francisco Bay area: Pacific Section, Society for Sedimentary Geology 

Book 76.

Shacklette, H.T.; Boerngen, J.G. 1984. Element concentrations in soils and other surficial 

materials of the conterminous United States: U.S. Geological Survey Professional Paper 

1270.

San Francisco Regional Water Quality Control Board (SFRWQCB) 2015. Total Maximum 

Daily Load: Selenium in North San Francisco Bay, Staff Report. Retrieved November 2015 

from: 

<http://www.waterboards.ca.gov/sanfranciscobay/water_issues/programs/TMDLs/seleniumt

mdl.shtml>

State Water Resources Control Board (SWRCB) 2012. 2012 Clean Water Act Section 303(d) 

and 305(b) Integrated Report. Retrieved November 2015 from 

<http://www.waterboards.ca.gov/water_issues/programs/tmdl/integrated2012.shtml> 

San Francisco Estuary Project, 2007. Comprehensive Conservation and Management Plan
REFERENCES

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 44

United States Environmental Protection Agency (USEPA) 1979. Estimating Water Treatment 

Costs: Volume 2 Cost Curves Applicable to 1 to 200 mgd Treatment Plants. EPA-600/2-79-

162b.

United States Environmental Protection Agency (USEPA) 1983. Treatability Manual: 

Volume 1 Treatability Data. EPA-600/8-80-042a.

United States Environmental Protection Agency (USEPA) 2008. Municipal Nutrient 

Removal Technologies Reference Document: Volume 1 & 2 - Technical Report. (EPA 832-

R-08-006).

United Stated Environmental Protection Agency (USEPA) 2015. Draft Aquatic Life Ambient 

Water Quality Criterion for Selenium – Freshwater. EPA 822-P-15-001.

United States Environmental Protection Agency (USEPA) 2016. Aquatic Life Ambient 

Water Quality Criterion for Selenium – Freshwater. EPA XXX-X-16-XXX. 

Yee, D. (2012) Technical Memorandum: Selenium Fractionation and Speciation in Final 

Effluents of Selected San Francisco Bay Area Municipal Wastewater Treatment Facilities. 

San Francisco Estuary Institute. Retrieved November 2015 from: 

<http://www.sfei.org/documents/selenium-fractionation-and-speciation-final-effluentsselected-san-francisco-bay-area-muni>
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 45

Appendix A – Facility Analyses

This appendix provides detailed analyses for the 16 sample facilities in alphabetical order, 

with municipal dischargers first followed by industrial dischargers. For each facility, under 

the baseline scenario (i.e. using the current criteria) and the revised criteria scenario, EPA 

conducted an RPA, identified potential compliance scenarios, and estimated the associated 

costs. Since the effluent data used by EPA to determine reasonable potential, effluent 

limitations, and compliance actions and costs may be more recent than the effluent data used 

to develop the existing permits, there may be some cases where EPA’s analysis indicates 

some requirements and costs for a facility under the baseline scenario that are not reflected in 

the existing permit for the facility. Such costs would not be attributable to the proposed 

revised criteria, but rather would be baseline costs attributable to the existing criteria. Only 

compliance actions and costs that would be needed above the baseline level of controls are 

attributable to the proposed revised criteria. 

A.1 City of Burlingame and North Bayside Systems Unit

The treatment facility for the City of Burlingame and North Bayside Systems Unit (Plant; 

NPDES permit No. CA0037788) is located south of the San Francisco International Airport 

and northeast of the City of Burlingame. The Plant provides secondary treatment of domestic 

and commercial wastewater for the City of Burlingame, a portion of the Town of

Hillsborough, and the Burlingame Hills Sewer maintenance District, a total population of 

approximately 37,000. No significant industrial users discharge to the Plant. The Plant design 

average daily dry weather flow is 5.5 mgd and the peak wet weather capacity, based on the 

engineered contractual limit for the North Bayside System Unit (NBSU) forcemain, is 16 

mgd. The Plant discharges to Lower San Francisco Bay. 

Treatment Processes

Treatment consists of screening, grit removal, primary sedimentation, secondary biological 

treatment, secondary clarification, and chlorine disinfection. Treated water undergoes 

dechlorination at the South San Francisco and San Bruno Water Quality Control Plant prior 

to discharge to Lower San Francisco Bay.

During wet weather, primary effluent flows in excess of 13 mgd are directed to the Facility’s 

2.38 million gallon onsite temporary storage units. When the storage units reach their 

maximum capacity, primary effluent flows in excess of 13 mgd are blended with secondary 

effluent, disinfected, and discharged to the NBSU forcemain. Stored water from the 

temporary storage facilities is returned to the primary clarifier for full treatment after the 

influent flow subsides to a level protective of secondary treatment processes. The Plant is 

permitted to discharge an average dry weather flow of 5 mgd.

Effluent Data 

Exhibit A- 1 summarizes selenium effluent data for the treated wastewater between September 

2011 and September 2015. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 46

Exhibit A- 1. Summary of Selenium Effluent Data: City of Burlingame WWTP

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

23 5 0.534 0.407 0.217 1

Source: California Integrated Water Quality System

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on the existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 1 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the proposed 

water quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 1. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed water column criterion), EPA did not consider 

dilution, and instead calculated end-of-pipe limitations. Under the proposed criterion, the 

discharger would have to meet an AMEL of 0.17 μg/L and MDEL of 0.30 μg/L. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 47

Since the MEC is above the QL, EPA assumed that the Plant will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). According to the existing permit, the Plant does not currently use iron salt 

chemical addition or media filtration unit processes. Therefore, EPA has developed a cost 

estimate to install a chemical treatment system and sand filters using the cost curves 

described in Section 4.4. Using a flow rate of 5.5 mgd, the estimated installed capital cost for 

the Plant is approximately $6.2 million and the estimated annual O&M cost is $260,000.

A.2 City of Livermore and EBDA

The WWTP for the City of Livermore and EBDA (Plant; NPDES Permit No. CA0038008) 

serves approximately 83,600 people from the City of Livermore. The Plant provides 

secondary treatment for up to 8.5 mgd. During high flow events, a side flow weir in the 

influent manhole structure diverts peak untreated wastewater flows to a 15 million gallon 

emergency holding basin. Additionally, an average of 1.3 mgd of wastewater receives 

tertiary treatment and is used as recycled water and sent to the Zone 1 Distribution System. 

The Plant has a current permitted average dry weather design flow of 8.5 mgd, a future 

average dry weather design flow of 11.1 mgd, and a contractual peak wet weather design 

flow of 12.4 mgd. The Plant discharges to Lower San Francisco Bay.

Treatment Processes

The 2012 Permit fact sheet reports that treatment consists of screening, grit removal, preaeration, primary clarification with ferric chloride addition for hydrogen sulfide control in the 

digestion process, activated sludge, secondary clarification and disinfection using sodium 

hypochlorite. The tertiary treated wastewater is diverted after the secondary clarifiers and 

routed through in-line granular media filtration and ultraviolet disinfection. Sludge is 

anaerobically digested, dewatered using belt filter presses, and trucked offsite.

Effluent Data 

Exhibit A- 2 summarizes selenium effluent data for the treated wastewater between March 

2011 and July 2015. 

Exhibit A- 2. Summary of Selenium Effluent Data: City of Livermore Water Reclamation Plant

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

53 50 0.5671 0.501 0.284 1.7

Source: California Integrated Water Quality System

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. A CV of 0.6 was used to calculate Water Quality-Based Effluent Limitations due to the limited 

number of detected observations.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 48

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on the existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 1.7 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the proposed 

water quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 2. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.16 μg/L and MDEL of 0.33 μg/L. 

Since the MEC is above the QL, EPA assumed that the Plant will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). According to the existing permit, the Plant does not currently use iron salt 

chemical addition or media filtration unit processes. Therefore, EPA has developed a cost 

estimate to install a chemical treatment system and sand filters using the cost curves 

described in Section 4.4. Using a flow rate of 8.5 mgd, the estimated installed capital cost for 

the Plant is approximately $7.6 million and the estimated annual O&M cost is $310,000. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 49

A.3 City of Millbrae and North Bayside Systems Unit 

The WWTP for the City of Millbrae and North Bayside Systems Unit (Plant; NPDES Permit 

No. CA0037532) provides primary and secondary treatment of wastewater for the City of 

Millbrae and serves a population of about 21,500. The Plant has a permitted average dry 

weather design capacity of 3.0 mgd and can process up to 9.0 mgd of wastewater during wet 

weather. The Plant discharges to Lower San Francisco Bay.

Treatment Processes

The 2013 permit fact sheet reports that treatment processes include a headworks with coarse 

and fine bar screens and grit removal, primary sedimentation in rectangular clarifiers, 

biological activated sludge treatment, secondary clarification, disinfection with sodium 

hypochlorite, and final effluent skimming. Effluent is dechlorinated prior to discharge into 

Lower San Francisco Bay.

Effluent Data 

Exhibit A- 3 summarizes selenium effluent data for the treated wastewater between November 

2011 and November 2014. 

Exhibit A- 3. Summary of Selenium Effluent Data: City of Millbrae and North Bayside Systems 

Unit

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

7 2 0.3161 0.353 0.112 0.482

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. A CV of 0.6 was used to calculate Water Quality-Based Effluent Limitations due to the limited 

number of detected observations.

2. The max result was detected but not quantified (DNQ; i.e., selenium was detected in the sample 

but at levels too low to accurately quantify—the reported concentration is a best estimate).

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 50

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 0.48 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the proposed 

water quality criterion. 

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 3. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.16 μg/L and MDEL of 0.33 μg/L. 

Since the MEC for the Plant is below the QL, EPA assumed that it is discharging near the 

projected limitations and that compliance is likely to be achievable using process 

optimization methods (see Section 4.4). EPA developed one-time costs for implementing a 

process optimization study of $52,000. 

A.4 City of San Mateo/Foster City Estero

The WWTP for the City of San Mateo/Foster City Estero Municipal Improvements District 

(Plant; NPDES Permit No. CA0037541) provides secondary and advanced secondary 

treatment of domestic, commercial, and industrial wastewater for the City of San Mateo, the 

City of Foster City, the Town of Hillsborough, and portions of the City of Belmont and 

unincorporated San Mateo County. The Plant serves a population of approximately 139,000, 

and has an average daily dry weather design flow of 15.7 mgd and a peak wet weather design 

flow for secondary treatment of 40 mgd. The Plant discharges to Lower San Francisco Bay.

Treatment Processes

The 2013 permit fact sheet states that treatment at the Plant consists of primary 

sedimentation, secondary biological treatment through aeration basins, secondary 

clarification, chlorine disinfection, and dechlorination using sodium bisulfite, as well as the 

option of pressure filters when necessary to comply with effluent limitations.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 51

Effluent Data 

Exhibit A- 4 summarizes selenium effluent data for the treated wastewater between June 2011 

and March 2015. 

Exhibit A- 4. Summary of Selenium Effluent Data: City of San Mateo WWTP

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

44 2 0.578 0.215 0.124 0.531

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. The max result was reported as detected but not quantified (DNQ; i.e., selenium was detected in the 

sample but at levels too low to accurately quantify—the reported concentration is a best estimate).

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 

20 μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario.

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 0.53 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the proposed 

water quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 4. Due to an absence of assimilative 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 52

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.18 μg/L and MDEL of 0.29 μg/L. 

Since the MEC for the Plant is below the QL, EPA assumed that it is discharging near the 

projected limitations and that compliance is likely to be achievable using process 

optimization methods (see Section 4.4). EPA developed one-time costs for implementing a 

process optimization study of $52,000. 

A.5 Dublin San Ramon Services District 

The WWTP for the Dublin San Ramon Services District (Plant; NPDES Permit No. 

CA0037613) serves the City of Dublin, the city of Pleasanton, and the southern portion of the 

City of San Ramon, a service area population of approximately 131,900 people. The Plant 

has an average dry weather flow design capacity of 17 mgd from the Dublin San Ramon 

Services District, plus 3.2 mgd of Zone 7 groundwater RO reject flow (i.e., a total of 20.2 

mgd). Treated effluent is discharged to Lower San Francisco Bay.

Treatment Processes

The 2012 Permit fact sheet reports that treatment consists of screening, grit removal, primary 

clarification, activated sludge, secondary clarification, and disinfection using sodium 

hypochlorite. 

Effluent Data 

Exhibit A- 5 summarizes selenium effluent data for the treated wastewater between March 

2011 and July 2015. 

Exhibit A- 5. Summary of Selenium Effluent Data: Dublin San Ramon Services District WWTP

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

53 12 0.896 1.218 1.091 4.7

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 53

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 4.7 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the proposed 

water quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 5. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.15 μg/L and MDEL of 0.36 μg/L. 

Since the MEC is above the QL, EPA assumed that the Plant will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). According to the existing permit, the Plant does not currently use iron salt 

chemical addition or media filtration unit processes. Therefore, EPA has developed a cost 

estimate to install a chemical treatment system and sand filters using the cost curves 

described in Section 4.4. Using a flow rate of 20.2 mgd, the estimated installed capital cost 

for the Plant is approximately $13.2 million and the estimated annual O&M cost is $520,000.

A.6 East Bay Dischargers Authority, Joint Outfall

East Bay Dischargers Authority (EBDA; NPDES No. CA0037869) is a Joint Exercise of 

Power Agency, the members of which separately own and operate collection and treatment 

facilities for domestic, commercial, and industrial wastewater. EBDA is comprised of five 

member agencies: City of Hayward, Oro Loma Sanitary District, Castro Valley Sanitary 

District, City of San Leandro, and Union Sanitary District. EBDA conveys treated 

wastewater from its member agencies’ three treatment facilities together with treated 

wastewater from the Livermore-Amador Valley Water Management Agency’s treatment 

plant, which is comprised of treated wastewater from the City of Livermore, to a 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 54

dechlorination station near the San Leandro Marina (collectively, these treatment plants will 

be referred to as the Plants, hereinafter). The total permitted average dry weather flow to be 

discharged at the EBDA Common Outfall is 107.8 mgd, and the total peak daily wet weather 

flow is 189.1 mgd. EBDA discharges to Lower San Francisco Bay.

Treatment Processes

The 2012 Permit fact sheet reports that treatment consists of dechlorination of the combined 

treated wastewater by sodium bisulfite before discharge from the common outfall to Lower 

San Francisco Bay. Treatment at the City of Wayward Water Pollution Control Facility 

consists of comminution, grit removal, primary sedimentation, flow equalization, high-rate 

trickling filtration, secondary clarification, and chlorination. Treatment at the Oro Loma and 

Castro Valley Sanitary Districts’ treatment facility consists of screening, grit removal, 

primary sedimentation, activated sludge, secondary clarification, and chlorination. Treatment 

at the San Leandro Water Pollution Control Plant grinding, primary sedimentation, trickling 

filter, activated sludge, secondary clarification, and disinfection by sodium hypochlorite. 

Treatment at the Union Sanitary District consists of screening, primary sedimentation, 

activated sludge, secondary clarification, and chlorination

Effluent Data 

Exhibit A- 6 summarizes selenium effluent data for the treated wastewater between April 

2011 and July 2015. 

Exhibit A- 6. Summary of Selenium Effluent Data: East Bay Dischargers Authority Common 

Outfall

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

53 9 0.575 0.523 0.301 1.2

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 55

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 1.2 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the proposed 

water quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 6. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.17 μg/L and MDELof 0.30 μg/L. 

Since the MEC is above the QL, EPA assumed that the facility will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). The Joint Outfall services a number of dischargers and the available 

information on their treatment processes indicated that none of the plants utilized iron salt 

chemical addition or media filtration. Therefore, EPA has developed a cost estimate to install 

a chemical treatment system and sand filters using the cost curves described in Section 4.4 at 

each of the plants. Since the cost curves are based on a linear trend of the costs for EPA’s 

model treatment trains, costs may be estimated using an aggregate flow rate for the Joint 

Outfall (i.e., cost based on an aggregate flow rate will be equal to that estimated based on 

individual contributing systems). Using a flow rate of 107.8 mgd, the estimated installed 

capital cost for the Plants is approximately $54.7 million and the estimated annual O&M cost 

is $2.1 million.

A.7 East Bay Municipal Utility District, Wet Weather Facilities

East Bay Municipal Utility District, Special District No. 1 is the owner and operator of three 

wet weather facilities (WWF) known as the Point Isabel WWF, the San Antonio Creek 

WWF, and the Oakport WWF (collectively, the Facility, NPDES Permit No. CA0038440). 

The WWFs are connected to an interceptor system with a hydraulic capacity of 760 mgd and 

a million-gallon wet weather storage basin along one of the interceptors.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 56

Treatment Processes

If influent flows at the Point Isabel WWF persist to the point of taking up the storage 

capacity of the units, the WWF provides treatment consisting of coarse screens, bar screens, 

grit chambers, and sedimentation/disinfection basins. 

Treatment at the San Antonio Creek WWF consists of grit removal, fine screening, and 

disinfection.

If influent flows persist to the point of taking up the storage capacity of the units, the Oakport 

WWF provides treatment consisting of coarse screens and sedimentation/disinfection basins.

Effluent Data 

As of 2009, discharge from this Facility has been prohibited. This prohibition is included in 

the existing permit (Permit No. R2-2014-0044; NPDES Permit No. CA0038440). As such 

effluent data for the Facility is not available.

Receiving Water

All discharges from the Facility are prohibited, and as such there is no applicable receiving 

water.

Baseline Scenario

All discharges from the Facility are prohibited and, therefore, no effluent limitations are 

applicable under the baseline scenario. 

Proposed Criteria Scenario

All discharges from the Facility are prohibited and, therefore, no effluent limitations are 

applicable under the proposed criteria, and the facility would incur no costs.

A.8 East Bay Regional Park District, Hayward Marsh

The WWTP for the Regional Park District, Union Sanitary District, and East Bay 

Dischargers Authority at Hayward Marsh (Plant; NPDES Permit No. CA0038636) is a 145-

acre improved marsh system which includes three freshwater marsh basins (85 acres) and 

two brackish water basins (60 acres) adjacent to Lower San Francisco Bay. Approximately 

2.6 mgd is diverted from the Alvarado WWTP in Union City as the freshwater source for the 

Marsh. The three freshwater marsh basins are part of the treatment process, and thus part of 

the treatment facility. The two brackish water basins and San Francisco Bay are the receiving 

waters and waters of the United States within the South San Francisco Bay Basin watershed. 

The Marsh has a hydraulic capacity of 20 mgd. Hayward Marsh is operated to enhance the 

beneficial uses of reclaimed wastewater, to derive net environmental benefits, and as a 

research site to better understand development and management of a marsh using reclaimed 

wastewater.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 57

Treatment Processes

Treatment at the Plant consists of screening, primary sedimentation, activated sludge, 

secondary clarification, and chlorination/disinfection of final effluent. Sludge is 

anaerobically digested, dewatered using centrifuge processes, and disposed of at an 

authorized disposal site. Most of the treated effluent is transported to the East Bay 

Dischargers pipeline where it mixes with treated effluent from other EBDA agencies and is 

transported to a dechlorination station near the San Leandro Marina. This treated effluent is 

transported to EBDA’s deepwater outfall in Lower San Francisco Bay west of the Oakland 

Airport. That discharge is regulated under NPDES Permit No. CA0037869. Approximately 

2.6 mgd is diverted to Hayward Marsh and is regulated under the permit in question (NPDES 

No. CA0038636). Secondary effluent enters a system of three freshwater marsh basins and 

two brackish water basins. The hydraulic capacity of the marsh system is 20 mgd. The 

brackish water basins discharge the final effluent into Lower San Francisco Bay.

Effluent Data 

Recent effluent data for this permittee was not available for analysis. Instead, EPA utilized 

the MEC and effluent descriptive statistics reported in the discharger’s 2011 permit (Permit 

No. R2-2011-0058; NPDES No. CA0037834). Exhibit A- 7 summarizes the information 

reported in the 2011 permit.

Exhibit A- 7. Summary of Selenium Effluent Data: East Bay Regional Park District

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

N/A N/A N/A1 N/A N/A 0.55

N/A = Not Available

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. A CV of 0.6 was used to calculate Water Quality Based Effluent Limitations due to the limited 

number of detected observations.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 58

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criterion. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). As with 

the baseline scenario, EPA based the analysis on the analytical approaches described in Section 4.2. 

The MEC (i.e., 0.55 μg/L) exceeds the proposed criterion and, therefore, the discharge has reasonable 

potential to cause or contribute to the exceedance of the water quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the effluent 

coefficient of variation described in Exhibit A- 7. Due to an absence of assimilative capacity (i.e., the 

B exceeded the proposed criterion), EPA did not consider dilution, and instead calculated end-of-pipe 

limitations. Under the proposed criterion, the discharger would have to meet an AMEL of 0.16 μg/L 

and MDEL of 0.33 μg/L. 

Since the MEC for the Plant is below the QL, EPA assumed that it is discharging near the projected 

limitations and that compliance is likely to be achievable using process optimization methods (see 

Section 4.4). EPA developed one-time costs for implementing a process optimization study of 

$52,000. 

A.9 Palo Alto Regional Water Quality Control Plant

The Palo Alto Regional Water Quality Control Plant and the City of Palo Alto wastewater 

collection system (collectively, the facility; NPDES Permit No. CA0037834) provides 

advanced secondary treatment of domestic, commercial, and industrial wastewater collected 

from the cities of Los Altos, Los Altos Hills, Palo Alto, and Mountain View; the East Palo 

Alto Sanitary District; and the unincorporated area of the Stanford University Campus. The 

service area population is approximately 220,000, and the Facility’s design flow rate is 39 

mgd. Approximately 95% of the treated final effluent that is not recycled is discharged to an 

unnamed channel that leads to South San Francisco Bay. The remaining 5% is discharged to 

Matadero Creek, which flows into Mayfield Slough and then into South San Francisco Bay at 

the Flood Basin tide gates.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 59

Treatment Processes

The 2014 Permit Fact Sheet reports that treatment processes include screening and grit 

removal, primary sedimentation, biological treatment, secondary clarification, filtration, and 

disinfection.

Effluent Data

Exhibit A- 8 summarizes selenium effluent data for the treated wastewater between March 

2011 and June 2015. 

Exhibit A- 8. Summary of Selenium Effluent Data: Palo Alto Regional Water Quality Control 

Plant

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

58 0 0.418 1.456 0.608 2.6

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

Receiving Water

The facility discharges to South San Francisco Bay. The SFRWQCB utilized the Dumbarton 

Bridge monitoring station (station number BA 30) for purposes of background receiving 

water characterization. The available ambient receiving water monitoring data was collected 

from the Yerba Buena Island monitoring station between 1993 and 2013. The maximum total 

recoverable selenium concentration observed during this period was 0.628 μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 2.6 μg/L) exceeds the proposed criterion and, therefore, the 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 60

discharge has reasonable potential to cause or contribute to the exceedance of the water 

quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 88. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.19 μg/L and MDEL of 0.25 μg/L. 

Since the MEC is above the QL, EPA assumed that the facility will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). According to the existing permit, the facility does not currently use iron salt 

chemical addition but does have a media filtration unit process. Therefore, EPA has 

developed a cost estimate to install a chemical treatment system using the cost curves 

described in Section 4.4. Using a flow rate of 39 mgd, the estimated installed capital cost for 

the Plant is approximately $13.0 million and the estimated annual O&M cost is $370,000. 

A.10 Cities of San Jose and Santa Clara

The WWTP for the Cities of San Jose and Santa Clara (Plant; NPDES Permit No. 

CA0037842) provides advanced-secondary treatment of wastewater from domestic, 

commercial, and industrial sources. Ownership of the Plant by the City of San Jose and City 

of Santa Clara was established under the original Joint Powers agreement. Through a series 

of additional “Master Agreements for Wastewater Treatment,” five additional satellite 

collection systems obtained rights to a share of the treatment capacity to treat their 

discharged sewage, including the City of Milpitas, Burbank Sanitation District, Cupertino 

Sanitation District, West Valley Sanitation District, and Santa Clara County Sanitation 

Districts Nos. 2 and 3. The Plant serves a population of approximately 1.4 million and has an 

average daily dry weather design flow of 167 mgd and a peak daily wet weather design flow 

of 261 mgd. The Plant discharges to the Artesian Slough.

Treatment Processes

The 2013 Permit Fact Sheet reports that the Plant provides treatment consisting of influent 

screening and grit removal; primary clarification; secondary treatment with an activated 

sludge process with two parallel aeration basin treatment trains configured and operated for 

biological nutrient removal (BNR); secondary clarifiers; dual media gravity filtration; and 

disinfection with chlorine, ammonia removal, and dechlorination using sulfur dioxide.

Effluent Data 

Exhibit A- 9 summarizes selenium effluent data for the treated wastewater between November 

2011 and November 2014. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 61

Exhibit A- 9. Summary of Selenium Effluent Data: San Jose/Santa Clara Water Pollution 

Control Plant

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

52 0 0.486 0.474 0.231 0.7

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

Receiving Water

The facility discharges to South San Francisco Bay. The SFRWQCB utilized the Dumbarton 

Bridge monitoring station (station number BA30) for purposes of background receiving 

water characterization. The available ambient receiving water monitoring data was collected 

from the Yerba Buena Island monitoring station between 1993 and 2013. The maximum total 

recoverable selenium concentration observed during this period was 0.628 μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 

20 μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 0.7 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the water 

quality criterion. 

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 9. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.18 μg/L and MDEL of 0.26 μg/L. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 62

Since the MEC for the Plant is below the QL, EPA assumed that it is discharging near the 

projected limitations and that compliance is likely to be achievable using process 

optimization methods (see Section 4.4). EPA developed one-time costs for implementing a 

process optimization study of $52,000. 

A.11 South Bayside System Authority, Wastewater Treatment Plant

The South Bayside System Authority WWTP (Plant; NPDES Permit No. CA0038369) 

provides advanced secondary treatment of domestic, commercial, and industrial wastewater 

for the cities of Belmont, San Carlos, Redwood City, and Woodside; and for the service area 

of the west Bay Sanitary District, which collects wastewater from the cities of Menlo Park, 

Atherton, and Portola Valley, and areas of East Palo Alto, Woodside, and unincorporated San 

Mateo and Santa Clara counties. The service area population is approximately 199,000. The 

Plant has an average dry weather design flow of 29 mgd, and a peak wet weather design flow 

of 71 mgd, and discharges to Lower San Francisco Bay.

Treatment Processes

The 2012 Permit fact sheet reports treatment processes consist of primary sedimentation, 

secondary biological treatment through fixed film reactors and aeration basins, secondary 

clarification, mono- or dual-media filtration, chlorine disinfection, and dechlorination using 

sodium bisulfite. 

Effluent Data

Exhibit A- 10 summarizes selenium effluent data for the treated wastewater between January 

2011 and December 2014. 

Exhibit A- 10. Summary of Selenium Effluent Data: South Bayside System Authority WWTP

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

35 1 0.591 0.317 0.187 0.771

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. The max result was detected below the method quantification level and reported as an estimated 

concentration.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 63

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 0.77 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the water 

quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 10. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.17 μg/L and MDEL of 0.30 μg/L. 

Since the MEC for the Plant is below the QL, EPA assumed that it is discharging near the 

projected limitations and that compliance is likely to be achievable using process 

optimization methods (see Section 4.4). EPA developed one-time costs for implementing a 

process optimization study of $52,000. 

A.12 Cities of South San Francisco, San Bruno, and the North Bayside 

Systems Unit

The WWTP for the Cities of South San Francisco, San Bruno, and the North Bayside 

Systems Unit (Plant; NPDES No. CA0038130) provides primary and secondary wastewater 

treatment. The Plant serves an approximate population of 110,500, and has an average daily 

dry weather design flow of 13 mgd. The Plant discharges to Lower San Francisco Bay.

Treatment Processes

The 2014 Permit fact sheet reports that treatment consists of bar screens and two grit removal 

systems, and, during dry weather, treatment with ferric chloride and polymer for flocculation 

and primary clarifiers for removal of grease, floating solids, and settable solids. Further 

treatment includes aeration basins and secondary clarifiers, disinfection with sodium 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 64

hypochlorite, blending with chlorinated effluent, and chlorine neutralization with sodium 

bisulfite. During wet weather, when influent flow greatly exceeds the peak secondary 

treatment capacity (30 mgd design capacity), primary effluent may be routed around the 

aeration basins and secondary clarifiers and blended with secondary-treated effluent.

Effluent Data 

Exhibit A- 11 summarizes selenium effluent data for the treated wastewater between June 

2011 and July 2015. 

Exhibit A- 11. Summary of Selenium Effluent Data: South San Francisco/San Bruno Water 

Quality Control Plant

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

52 1 0.659 1.219 0.804 2.7

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 2.7 μg/L) exceeds the proposed criterion and, therefore, the 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 65

discharge has reasonable potential to cause or contribute to the exceedance of the water 

quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 11. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.17 μg/L and MDEL of 0.32 μg/L. 

Since the MEC is above the QL, EPA assumed that the Plant will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). According to the existing permit, the Plant does not currently use media 

filtration but does use iron salts addition in their treatment process. Therefore, EPA has 

developed a cost estimate to install a media filtration system using the cost curves described 

in Section 4.4. Using a flow rate of 13 mgd, the estimated installed capital cost for the Plant 

is approximately $4.1 million dollars and the estimated annual O&M cost is $230,000.

A.13 San Francisco Southeast Plant

The City and County of San Francisco is the owner and operator of the Southeast Water 

Pollution Control Plant (Southeast Plant), North Point Wet Weather Facility (North Point 

Facility), Bayside Wet Weather Facilities, and the wastewater collection system (collectively 

Facility; NPDES Permit No. CA0037664). The Facility serves eastern San Francisco and 

portions of Brisbane and Daly City, and has a service population of approximately 580,000. 

The Southeast Plant provides primary and secondary treatment of combined wastewater and 

storm water, and has an average dry weather design flow capacity of 85.4 mgd and a wet 

weather design flow capacity of 250 mgd. The North Point Facility provides primary 

treatment of combined wastewater and storm water during wet weather and has a wet 

weather design flow capacity (primary treatment only) of 150 mgd. The Bayside Wet 

Weather Facilities provide equivalent-to-primary treatment during wet weather. The Facility 

discharges to San Francisco Bay.

Treatment Processes

During dry weather, the Southeast Plant provides secondary wastewater treatment. The 

treatment processes include a headworks with coarse and fine bar screens, and grit removal; 

primary sedimentation tanks; pure oxygen aeration basins; secondary clarifiers; and chlorine 

contact basins for chlorination using sodium hypochlorite and dechlorination using sodium 

bisulfite. During wet weather up to 150 mgd receives both primary and secondary treatment; 

the remaining flow (up to 100 mgd) receives only primary treatment. The entire volume is 

disinfected prior to discharge.

The North Point Facility discharges only during wet weather. The treatment consists of bar 

screens, sedimentation tanks equipped with skimmers, sodium hypochlorite injection, and 

dechlorination using sodium bisulfite addition. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 66

During dry weather the Bayside Wet Weather Facilities transport wastewater to the Southeast 

Plant. During wet weather, these structures transfer combined wastewater to the Southeast 

Plant and, if necessary, the North Point Facility. They also provide storage for more than 120 

million gallons of combined wastewater. In the event that the capacities of the Southeast 

Plant, North Point Facility, and storage/transport structures are exceeded, the combined 

wastewater receives the equivalent of primary treatment consisting of settling solids with a 

series of baffles and weirs that also remove floatable materials prior to discharge. 

Effluent Data 

Exhibit A- 12 summarizes selenium effluent data for the treated wastewater between January 

2011 and December 2014. 

Exhibit A- 12. Summary of Selenium Effluent Data: San Francisco Southeast Plant

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

49 3 0.679 0.251 0.171 1.1691

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. The max result was detected below the method quantification level and reported as an estimated 

concentration.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 67

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 1.169 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the water 

quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 12. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criterion, the discharger would 

have to meet an AMEL of 0.16 μg/L and MDEL of 0.33 μg/L. 

Since the MEC is above the QL, EPA assumed that the Plant will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). According to the existing permit, the Plant does not currently have an iron salts 

addition or media filtration unit processes. Therefore, EPA has developed a cost estimate to 

install chemical treatment and a media filtration system using the cost curves described in 

Section 4.4. Using a flow rate of 84.5 mgd, the estimated installed capital cost for the Plant is 

approximately $43.7 million and the estimated annual O&M cost is $1.7 million.

A.14 City of Sunnyvale

The Sunnyvale Water Pollution Control Plant (Plant; NPDES Permit No. CA0037621) 

provides advanced-secondary treatment of wastewater from domestic, commercial, and 

industrial sources from the City of Sunnyvale, Rancho Rinconada, and Moffett Field. The 

Plant serves a population of approximately 146,000, and has an average dry weather design 

flow capacity of 29.5 mgd and a peak wet weather design flow of 40 mgd. The Plant 

discharges to the Moffett Channel, which flows to South San Francisco Bay via Guadalupe 

Slough.

Treatment Processes

The 2014 Permit fact sheet reports that treatment includes grinding and grit removal, primary 

sedimentation, secondary treatment through the use of oxidation ponds, fixed-growth reactor 

nitrification, dissolved air flotation, dual media filtration, disinfection with chlorine gas, and 

dechlorination with sodium bisulfite.

Effluent Data 

Exhibit A- 13 summarizes selenium effluent data for the treated wastewater between April 

2011 and July 2015. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 68

Exhibit A- 13. Summary of Selenium Effluent Data: Sunnyvale Water Pollution Control Plant

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

70 60 0.6291 0.407 0.256 1.662

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. A CV of 0.6 was used to calculate Water Quality-Based Effluent Limitations due to the limited 

number of detected observations.

2. The max result was detected below the method Quantification Level and reported as an estimated 

concentration.

Receiving Water

The facility discharges to South San Francisco Bay. The SFRWQCB utilized the Dumbarton 

Bridge monitoring station (station number BA 30) for purposes of background receiving 

water characterization. The available ambient receiving water monitoring data was collected 

from the Yerba Buena Island monitoring station between 1993 and 2013. The maximum total 

recoverable selenium concentration observed during this period was 0.628 μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 1.66 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the water 

quality criterion.

Water quality-based effluent limitations were calculated according to the procedures 

described in Section 4.3 and using the effluent coefficient of variation described in Exhibit A13. Due to an absence of assimilative capacity (i.e., the B exceeded the proposed criterion), 

EPA did not consider dilution, and instead calculated end-of-pipe limitations. Under the 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 69

proposed criterion, the discharger would have to meet an AMEL of 0.16 μg/L and MDEL of 

0.33 μg/L. 

Since the MEC is above the QL, EPA assumed that the Plant will need to pursue 

conventional treatment methods to comply with the projected effluent limitations (see 

Section 4.4). According to the existing permit, the Plant does not currently use iron salts 

addition but does have media filter in their treatment process. Therefore, EPA has developed 

a cost estimate to install a chemical treatment system using the cost curves described in 

Section 4.4. Using a flow rate of 29.5 mgd, the estimated installed capital cost for the Plant is 

approximately $10.3 million and the estimated annual O&M cost is $290,000.

A.15 Bottling Group, LLC

The Bottling Group, Hayward Plant (Plant; NPDES Permit No. CA0030058) manufactures, 

bottles, and distributes drinking water and soft drinks. The Plant uses potable water supplied 

by the City of Hayward, which undergoes additional treatment in the manufacturing process. 

The treatment system is capable of treating up to 900,000 gallons of supply water with an 

80% recovery rate. The 20% of supply water not recovered is discharged in the RO

concentrate stream. The Plant has a maximum design treatment capacity of 900,000 gallons 

per day, and a permitted average monthly discharge rate of 143,000 gallons per day. The 

Plant discharges RO concentrate to the Alameda County Besco Pump Station, which pumps 

the effluent to the Alameda County flood control and Water Conservation District Flood 

Channel (the tidally-influenced downstream section of Old Alameda Creek) which flows to 

Lower San Francisco Bay.

Treatment Processes

The 2013 Permit fact sheet reports that treatment to filter supply water consists of anthracite 

and greensand filters to remove iron and manganese, 5-micrometer cartridge-filters, and 

finally RO membranes. The Plant adds chemical scale and fouling inhibitors to prevent 

fouling of the RO membranes and a dechlorinating agent. 

Effluent Data 

Exhibit A- 14 summarizes selenium effluent data for the treated wastewater from April 9, 

2015. 

Exhibit A- 14. Summary of Selenium Effluent Data: Bottling Group, Hayward Plant

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

1 1 N/A1 <0.2 N/A <0.2

CV = Coefficient of Variation

N/A = Not Available

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. 1. A CV of 0.6 was used to calculate Water Quality Based Effluent Limitations due to the limited 

number of detected observations.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 70

Receiving Water

The facility discharges to Alameda Creek, which flows into San Francisco Bay. The 

Discharger collects grab samples from Alameda Creek immediately upstream of the 

discharge location for purposes of background receiving water characterization. The 

available ambient receiving water monitoring data was collected from Alameda Creek on 

April 9, 2015. The total recoverable selenium concentration observed during this period was 

2.5 μg/L.

Baseline Scenario

The permit does not include any WQBELs based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria to confirm that no baseline 

WQBELs would be needed based on the analytical approaches described in Section 4.2. As 

neither the maximum effluent nor receiving water concentration exceed the existing criteria, 

this facility does not have reasonable potential to exceed the existing selenium criteria. 

Additionally, since there are no existing selenium WQBELs for this facility, EPA assumes 

that there is no reasonable potential under the third “trigger” which is activated when a 

review of other information (beyond the maximum effluent and ambient concentrations) 

suggests that limits are needed to protect beneficial uses. As such, EPA assumed that the 

facility would incur no costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column aquatic life selenium criterion

(0.2 μg/L). As with the baseline scenario, EPA based the analysis on the analytical 

approaches described in Section 4.2. Selenium was not detected in the available effluent 

monitoring data. Additionally, since there are no existing selenium WQBELs for this facility, 

EPA assumes that there is no reasonable potential under the third “trigger” which is activated 

when a review of other information (beyond the maximum effluent and ambient 

concentrations) suggests that limits are needed to protect beneficial uses. As such, EPA 

assumed that the facility would incur no costs under the proposed criteria.

A.16 San Francisco International Airport

The San Francisco International Airport, Mel Leong Treatment Plants (Plants; NPDES 

Permit No. CA0038318) include the Industrial Plant, which treats industrial wastewater from 

maintenance shops and vehicle washing, and first-flush stormwater runoff from industrial 

areas; and the Sanitary Plant, which includes a collection system and treats sanitary 

wastewater from airplanes and airport facilities, including terminal restrooms, hangars, 

restaurants, and shops. In emergency situations, either plant may be used to store or treat 

flows, spills, or overflows that would normally flow to the other plant to ensure that all 

wastewater is adequately treated. The service population for the Plants is estimated at 10,000. 

The Plants have a combined facility design flow of 2.2 mgd, and discharge to the Lower San 

Francisco Bay.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 71

Treatment Processes

The Sanitary Plant treatment operations consist of punched plate bar screens, grit removal, 

flow equalization, and chlorination. Solids from the Sanitary Plant are treated by gravity belt 

thickening and anaerobic digestion before dewatering by belt filter presses or air drying using 

sludge drying beds.

Treatment from the Industrial Plant includes flocculating the combined industrial wastewater 

and any incoming first flush storm water, dissolved air floatation, pH adjustment (as needed), 

aerobic biological treatment via trickling filter, secondary clarification, and chlorination. The 

Plant can divert up to 0.72 mgd of the effluent from the chlorination tank to tertiary filters. 

Sludge and scum are pumped to sludge beds for dewatering, and filtrate drained form the 

sludge is pumped back to the trickling filter for treatment. 

Chlorinated wastewater from both plants is combined for dechlorination at the South San 

Francisco Wastewater Treatment Facility

Effluent Data 

Exhibit A- 15 summarizes the available selenium effluent data for the treated wastewater 

between December 2010 and October 2015. 

Exhibit A- 15. Summary of Selenium Effluent Data: San Francisco International Airports, Mel 

Leong Treatment Plants

No. of Observations Effluent Summary (μg/L)

Total Nondetect CV Average Standard 

Deviation Max

2 0 0.1681 0.165 0.028 0.172

CV = Coefficient of Variation

μg/L = micrograms per liter

Concentrations are total recoverable form.

1. A CV of 0.6 was used to calculate Water Quality Based Effluent Limitations due to the limited 

number of detected observations.

Receiving Water

The facility discharges to Lower San Francisco Bay. The SFRWQCB utilized the Yerba 

Buena Island monitoring station (station number BC 10) for purposes of background 

receiving water characterization. The available ambient receiving water monitoring data was 

collected from the Yerba Buena Island monitoring station between 1993 and 2013. The 

maximum total recoverable selenium concentration observed during this period was 0.39 

μg/L.

Baseline Scenario

The existing permit (Permit No. R2-2013-0011; NPDES Permit No. CA0038318) includes an 

AMEL of 2.9 μg/L and a MDEL of 8.8 μg/L based on the existing chronic aquatic life 

selenium criterion (i.e., 5 μg/L) and the existing acute aquatic life selenium criterion (i.e., 20 

μg/L). EPA performed an RPA based on existing criteria using more recent data based on the 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 72

analytical approaches described in Section 4.2. As neither the maximum effluent nor 

receiving water concentration exceed the existing criteria, this facility does not have 

reasonable potential to exceed the existing selenium criteria. Since EPA found no reasonable 

potential using the most recent data and because the monitoring data demonstrated 

performance well below the existing WQBELs, EPA assumed that the facility would incur no 

costs under the baseline scenario. 

Proposed Criteria Scenario

EPA performed an RPA based on the proposed water column selenium criterion (0.2 μg/L). 

As with the baseline scenario, EPA based the analysis on the analytical approaches described 

in Section 4.2. The MEC (i.e., 0.172 μg/L) exceeds the proposed criterion and, therefore, the 

discharge has reasonable potential to cause or contribute to the exceedance of the water 

quality criterion.

WQBELs were calculated according to the procedures described in Section 4.3 and using the 

effluent coefficient of variation described in Exhibit A- 15. Due to an absence of assimilative 

capacity (i.e., the B exceeded the proposed criterion), EPA did not consider dilution, and 

instead calculated end-of-pipe limitations. Under the proposed criteria, the discharger would 

have to meet an AMEL of 0.16 μg/L and MDEL of 0.33 μg/L. 

Since the MEC for the Plants is below the QL, EPA assumed that it is discharging near the 

projected limitations and that compliance is likely to be achievable using process 

optimization methods (see Section 4.4). EPA developed one-time costs for implementing a 

process optimization study of $52,000. 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 73

Appendix B - Potential Compliance Costs, 7% Discount Rate

This appendix summarizes the point source compliance costs using a 7 percent discount rate 

as an alternative to the main analysis, presented in Section 4.4.2, which uses a 3 percent 

discount rate. For more details on the methodology for these analyses, see Section 4.

Exhibit B-1 summarizes the one-time (capital or process optimization) costs, O&M costs, 

and total annual cost for each of the identified facilities likely to have a control increment 

under the proposed selenium criterion. Exhibit B-2 summarizes the results of the sensitivity 

analysis (which includes additional costs for denitrification filters; as described in Section 

6.3). 
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 74

Exhibit B-1. Treatment and Estimated Cost Increment for Affected Facilities, 7% Discount Rate

NPDES 

Number Facility Name Capacity (mgd)

MEC 

(μg/L)

AMEL 

(μg/L)

One-Time

Cost O&M Cost Total Annual Cost

Municipal Facilities

CA0037621 City of Sunnyvale 29.5 1.66 0.16 $10,327,000 $293,000 $1,268,000

CA0037842 City of San Jose/Santa Clara 167 0.7 0.18 $52,000 -- $4,900

CA0037834 City of Palo Alto 39 2.6 0.19 $13,033,000 $367,000 $1,597,000

CA0038369 South Bayside System Authority 29 0.77 0.17 $52,000 -- $4,900

CA0037541 City of San Mateo/Foster City Estero 15.7 0.532 0.18 $52,000 -- $4,900

CA0038636 East Bay Regional Park District, 

Hayward Marsh 2.6 0.55 0.16 $52,000 -- $4,900

CA0037532 City of Millbrae and North Bayside 

Systems Unit 3 0.482 0.16 $52,000 -- $4,900

CA0037788 City of Burlingame and North Bayside 

Systems Unit 5.5 1 0.17 $6,194,000 $262,000 $847,000

CA0038130 Cities of South San Francisco, San 

Bruno, and North Bayside Systems Unit 13 2.7 0.17 $4,126,000 $229,000 $618,000

CA0038008 City of Livermore and EBDA 8.5 1.7 0.16 $7,617,000 $315,000 $1,034,000

CA0037613 Dublin San Ramon Services District, 

LAWMA, and EBDA 20.2 4.7 0.15 $13,169,000 $521,000 $1,764,000

CA0037869 East Bay Dischargers Authority, Joint 

Outfall 107.8 1.2 0.17 $54,734,000 $2,067,000 $7,234,000

CA0037664 San Francisco Southeast Plant 84.5 1.22 0.16 $43,679,000 $1,655,000 $5,778,000

CA0038440 East Bay Municipal Utility District, Wet 

Weather 158 -- -- $0 $0 $0

Subtotal $153,139,000 $5,709,000 $20,164,000

Industrial Facilities

CA0038318 San Francisco International Airport 2.2 0.1719 0.16 $52,000 -- $4,900

Subtotal $52,000 -- $4,900

Total $153,191,000 $5,709,000 $20,169,000
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 75

Exhibit B-1. Treatment and Estimated Cost Increment for Affected Facilities, 7% Discount Rate

NPDES 

Number Facility Name Capacity (mgd)

MEC 

(μg/L)

AMEL 

(μg/L)

One-Time

Cost O&M Cost Total Annual Cost

mgd = million gallons per day

μg/L = micrograms per liter

1. One-time costs annualized over 20 years using a 7 percent discount rate; see Section 4.4.2 for annualized results using a 3 percent discount 

rate.

2. Detected, but Not Quantified (DNQ); i.e., selenium was detected in the sample but at levels too low to accurately quantify; the reported 

concentration is a best estimate as determined by the laboratory instrumentation and methodology.
APPENDIX

Abt Associates Cost of Compliance with Selenium Criteria in San Francisco Bay and Delta ▌pg. 76

Exhibit B-2: End-of-Pipe Treatment Costs Sensitivity Analysis, 7% Discount Rate

NPDES 

Number Facility Name

Total Annual Cost1

Original2

Including Denitrification 

Filter

Municipal Facilities

CA0037621 City of Sunnyvale $1,268,000 $5,704,000

CA0037842 City of San Jose/Santa Clara3 $4,900 $4,900

CA0037834 City of Palo Alto $1,597,000 $7,461,000

CA0038369 South Bayside System Authority3 $4,900 $4,900

CA0037541 City of San Mateo/Foster City Estero3 $4,900 $4,900

CA0038636 East Bay Regional Park District, 

Hayward Marsh3

$4,900 $4,900

CA0037532 City of Millbrae and North Bayside 

Systems Unit3

$4,900 $4,900

CA0037788 City of Burlingame and North Bayside 

Systems Unit $847,000 $1,674,000

CA0038130

Cities of South San Francisco, San 

Bruno, and North Bayside Systems 

Unit

$618,000

$2,573,000

CA0038008 City of Livermore and EBDA $1,034,000 $2,312,000

CA0037613 Dublin San Ramon Services District, 

LAWMA, and EBDA $1,764,000 $4,801,000

CA0037869 East Bay Dischargers Authority, Joint 

Outfall $7,234,000 $23,444,000

CA0037664 San Francisco Southeast Plant $5,778,000 $18,484,000

CA0038440

East Bay Municipal Utility District, Wet 

Weather $0 $0

Subtotal $20,164,000 $66,477,500

Industrial Facilities

CA0038318 San Francisco International Airport3 $4,900 $4,900

Subtotal $4,900 $4,900

Total $20,169,000 $66,482,400

1. For plants discharging at levels above the most stringent quantitation level (1 μg/L), EPA assumed 

that POTWs will pursue conventional treatment methods to comply with the projected effluent 

limitations. POTWs operating below the quantitation level are discharging near the projected 

limitations and EPA has assumed that compliance is likely to be achievable using process 

optimization methods.

2. One-time costs annualized over 20 years using a 7 percent discount rate; for costs annualized 

using a 3 percent discount rate, see Section 6.3.

3. End-of-pipe treatment (including denitrification filter) is unnecessary for this facility, even 

considering alternative analytical detection limits.