CALIFORNIA ENVIRONMENTAL PROTECTION AGENCY

REGIONAL WATER QUALITY CONTROL BOARD

CENTRAL VALLEY REGION

Sacramento – San Joaquin 

Delta Estuary 

TMDL for 

Methylmercury 

Staff Report 

 

April 2010 

 
 

STATE OF CALIFORNIA 

Arnold Schwarzenegger, Governor 

CALIFORNIA ENVIRONMENTAL PROTECTION AGENCY 

Linda S. Adams, Secretary

REGIONAL WATER QUALITY CONTROL BOARD 

CENTRAL VALLEY REGION

Katherine Hart, Chair 

Cheryl K. Maki, Vice Chair 

Julian C. Isham, Member 

Karl E. Longley, Member 

Sandra O. Meraz, Member 

Dan Odenweller, Member 

Robert G. Walters, Member 

Pamela Creedon, Executive Officer

11020 Sun Center Drive #200 

Rancho Cordova, California 95670-6114 

Phone: (916) 464-3291 

eMail: info5@waterboards.ca.gov 

Web site: http://www.waterboards.ca.gov/centralvalley/ 

DISCLAIMER 

This publication is a report by staff of the California Regional Water Quality 

Control Board, Central Valley Region. This report contains the evaluation of 

alternatives and technical support for the adoption of a Basin Plan Amendment 

to the Water Quality Control Plan for the Sacramento and San Joaquin River 

Basins (Resolution No. R5-2010-0043). Mention of specific products does not 

represent endorsement of those products by the Central Valley Water Board. 

 
CALIFORNIA ENVIRONMENTAL PROTECTION AGENCY

REGIONAL WATER QUALITY CONTROL BOARD

CENTRAL VALLEY REGION

Sacramento – San Joaquin Delta Estuary 

TMDL for Methylmercury

Staff Report 

April 2010

REPORT PREPARED BY:

Michelle L. Wood 

Chris G. Foe, Ph.D. 

Janis Cooke, Ph.D. 

Stephen J. Louie 

 
 

ACKNOWLEDGEMENTS 

Central Valley Water Board staff gratefully acknowledges the valuable sampling, analytical and 

administrative support from: David Bosworth, Greg Marquis, Taro Murano and Dana Thomsen and 

Helena Kulesza, Andy Alexander, and Kelly Long (former staff and interns with the Mercury TMDL Unit). 

In addition, this report greatly benefited from the ideas and data generated by: 

Carrie Austin, Bill Johnson, Richard Looker (San Francisco Bay RWQCB); Jay Davis, Ben Greenfield, 

Jon Leatherbarrow and Lester McKee (San Francisco Estuary Institute); Mark Stephenson, Wes Heim 

and Amy Byington (Moss Landing Marine Laboratories); David Schoellhamer (USGS); 

Dan Russell (USFWS); Tom Schroyer (CDFG); Darell Slotton, Shaun Ayers, and Fraser Shilling 

(University of California, Davis); Stephen McCord (Larry Walker Associates); 

Khalil Abu-Saba (Brown & Caldwell); and Tom Grieb (Tetra Tech, Inc.).
SACRAMENTO – SAN JOAQUIN DELTA ESTUARY TMDL FOR METHYLMERCURY 

Staff Report 

EXECUTIVE SUMMARY 

This draft report presents California Regional Water Quality Control Board, Central Valley 

Region (Central Valley Water Board) staff recommendations for establishing a Total Maximum 

Daily Load (TMDL) for methylmercury in the Sacramento-San Joaquin Delta Estuary (the Delta). 

The report contains an analysis of the mercury impairment, a review of the primary sources, a 

linkage between methylmercury sources and impairments, and recommended mercury 

reductions to eliminate the impairment. 

This TMDL report is one component in the Central Valley Water Board’s water quality 

attainment strategy to resolve the mercury impairment in the Delta. The second component is 

implementing a control program through amendments to the Water Quality Control Plan for the 

Sacramento River and San Joaquin River Basins (the Basin Plan), as described in the proposed 

Basin Plan amendments and text in the draft Basin Plan Amendment staff report. 

Scope, Numeric Targets & Extent of Impairment 

In 1990 the Central Valley Water Board identified the Delta as impaired by mercury because fish 

had elevated levels of mercury that posed a risk for human and wildlife consumers. As a result, 

the Delta methylmercury TMDL addresses all waterways within the legal Delta boundary. In 

addition, the San Francisco Bay Regional Water Quality Control Board (San Francisco Water 

Board) identified Central Valley outflows via the Delta as one of the principal sources of total 

mercury to San Francisco Bay and, in its 2006 mercury TMDL for San Francisco Bay, assigned 

the Central Valley a load reduction of 110 kg/yr. Therefore, the final mercury TMDL control plan 

for the Delta must ensure protection of human and wildlife health in the Delta and meet the San 

Francisco Bay TMDL load allocation for the Central Valley. 

This TMDL report addresses both methyl and total mercury sources. Reductions in ambient 

aqueous methylmercury and methylmercury sources are required to reduce methylmercury 

concentrations in fish. The methylmercury linkage and source analyses divide the Delta into 

eight subareas based on the hydrologic characteristics and mixing of the source waters. 

Because the Yolo Bypass acts as a substantial source of methylmercury and total mercury to 

the Delta, the entire Yolo Bypass was included in the Yolo Bypass subarea. The Yolo Bypass is 

a 73,300-acre floodplain on the west side of the lower Sacramento River, about two thirds of 

which is within the legal Delta boundary. 

A separate methylmercury allocation scheme was developed for each subarea because the 

levels of impairment and the methylmercury sources in the subareas are substantially different. 

Reductions in total mercury loads are needed to reduce aqueous methylmercury in the Delta, to 

maintain compliance with the USEPA’s criterion of 50 ng/l, and to comply with the San 

Francisco Bay mercury control program. 

Delta Methylmercury TMDL Report April 2010 i
The concentration of methylmercury in fish tissue is the type of numeric target selected for the 

Delta methylmercury TMDL. Acceptable fish tissue levels of methylmercury for the trophic level 

(TL) food groups consumed by piscivorous wildlife species (that is, species that feed on fish) 

were calculated using a method developed by the U.S. Fish and Wildlife Service that uses daily 

intake levels, body weights and consumption rates. Numeric targets were developed to protect 

humans in a manner analogous to targets for wildlife using a method approved by the 

U.S. Environmental Protection Agency and Delta-specific information. 

Three numeric targets are recommended for the protection of humans and piscivorous wildlife: 

0.24 mg/kg (wet weight) in muscle tissue of large1

 trophic level four (TL4) fish such as bass and 

catfish; 0.08 mg/kg (wet weight) in muscle tissue of large TL3 fish such as carp and salmon; 

and 0.03 mg/kg (wet weight) in whole TL2 and TL3 fish less than 50 mm in length. The targets 

for large TL3 and TL4 fish are protective of (a) humans eating 32 g/day (8 ounces, uncooked 

fish per week) of commonly consumed, large fish; and (b) all wildlife species that consume large 

fish. The target for small TL2 and TL3 fish is protective of wildlife species that consume small 

fish. 

Elevated fish methylmercury concentrations occur along the periphery of the Delta while lower 

body burdens occur in the central Delta. Concentrations are greater than recommended as safe 

by the USFWS for wildlife in all subareas except in the Central Delta subarea. The Central 

Delta subarea requires no reduction to meet the proposed large TL3 fish target for human 

protection and an 8% reduction to meet the proposed large TL4 fish target for human protection. 

Percent reductions in fish methylmercury levels ranging from 0% to 75% in the peripheral Delta 

subareas will be needed to meet the numeric targets for wildlife and human health protection. 

Linkage 

The Delta linkage analysis focuses on the comparison of methylmercury concentrations in water 

and biota. Statistically significant, positive correlations have been found between aqueous 

methylmercury and aquatic biota, indicating that methylmercury levels in water is one of the 

primary factors determining methylmercury concentrations in fish. 

The Delta TMDL linkage focuses on the correlation between aqueous methylmercury and 

largemouth bass methylmercury because (1) largemouth bass was the only species 

systematically collected near many of the aqueous methylmercury sampling locations used to 

develop the methylmercury mass balance for the Delta (next section) and (2) largemouth bass 

is a useful bioindicator of spatial variation in mercury accumulation in the aquatic food chain 

because it maintains a localized home range and has a high trophic position in the Delta food 

web. It was possible to describe the recommended fish tissue targets in terms of the mercury 

concentration in standard 350 mm largemouth bass. A methylmercury concentration of 

0.28 mg/kg in 350 mm largemouth bass is equivalent to the target of 0.24 mg/kg for large TL4 

fish. A methylmercury concentration of 0.24 mg/kg in 350 mm largemouth bass is equivalent to 

the target of 0.08 mg/kg for TL3 fish. A methylmercury concentration of 0.42 mg/kg in 350 mm 

largemouth bass is equivalent to the target of 0.03 mg/kg for small fish. The methylmercury 

 

1

 Large fish are defined as 150-500 mm total length or legal catch length if designated by CDFG. 

Delta Methylmercury TMDL Report April 2010 ii
concentration of 0.24 mg/kg in bass predicted for the TL3 fish tissue target is the lowest of the 

bass values predicted for the three fish tissue targets and is therefore most likely protective of 

both human and wildlife consumers of higher and lower trophic level fish in the Delta. As a 

result, a methylmercury concentration of 0.24 mg/kg in 350 mm largemouth bass is referred to 

as the recommended implementation goal for largemouth bass. 

The mercury concentrations in standard 350-mm largemouth bass for each Delta subarea were 

regressed against the average unfiltered methylmercury concentrations in water in each Delta 

subarea. Substitution of the recommended implementation goal for largemouth bass 

(0.24 mg/kg) into the equation developed by this regression results in a predicted, average safe 

methylmercury concentration in ambient water of 0.066 ng/l. Incorporation of an explicit margin 

of safety of about 10% results in the recommended implementation goal for unfiltered ambient 

water of 0.06 ng/l methylmercury. This implementation goal would be applied as an annual 

average methylmercury concentration in ambient waters of the Delta. The recommended 

implementation goal is currently met in the Central Delta subarea and nearly met in the West 

Delta subarea. 

Sources – Methylmercury 

Average annual methylmercury inputs and exports were estimated for water years (WY) 2000 to 

2003, a relatively dry period that encompasses the available information. Sources of 

methylmercury in Delta waters include tributary inputs from upstream watersheds and withinDelta sources such as methylmercury flux from wetland and in-channel sediments, municipal 

and industrial wastewater, agricultural drainage, and urban runoff. Losses include water outflow 

to San Francisco Bay, exports to southern California, removal of dredged sediments, 

photodegradation, uptake by biota, and particle settling. Figure 1 illustrates the average daily 

methylmercury imports to and exports from the Delta and Yolo Bypass. Methylmercury flux from 

wetland and open water sediments within the Delta and Yolo Bypass accounts for about 35% of 

methylmercury inputs to the Delta/Yolo Bypass. Tributaries contribute about 58% of the 

Delta/Yolo Bypass methylmercury inputs. The difference between the sum of known inputs and 

exports is a measure of the uncertainty of the loading estimates and of the importance of other 

loss processes at work in the Delta. The sum of known water inputs and exports for WY2000-

2003 balances to within about 5%, indicating that all the major water inputs and exports have 

been identified. In contrast, the methylmercury budget for WY2000-2003 does not balance. 

Average annual methylmercury inputs and exports were approximately 14.3 g/day (5.2 kg/yr) 

and 6.7 g/day (2.5 kg/yr), respectively (Figure 1). Exports were only about 50% of inputs, 

indicating that the Delta acts as a net sink for methylmercury. Recent studies have shown that 

methylmercury photodegradation and particle settling can account for this with-Delta loss. 

Delta Methylmercury TMDL Report April 2010 iii
Figure 1: Average Daily Methylmercury Inputs to and Exports from the Delta/Yolo Bypass. 

The Delta/Yolo Bypass 

 Methylmercury 

Budget 

Municipal 

WWTPs 

0.6 

g/day 

SF Bay 

-4.7 g/day 

Ag 

Return 

Flows

0.3 

g/day 

Urban 

Runoff 

0.05 

g/day 

Atmospheric 

Dep. 

0.06 

g/day 

Wetlands

Sediment 

Flux 

2.7 

g/day 

Southern CA

-1.1 g/day 

Tributary 

Inputs 

8.2 g/day 

Open 

Water

Sediment 

Flux 

2.4 

g/day 

Photodegradation 

& Particle Settling

-7.6 g/day

Dredging 

-0.9 g/day 

Sources – Total Mercury & Suspended Sediment 

Sources of total mercury in the Delta and Yolo Bypass include tributary inflows from upstream 

watersheds, atmospheric deposition, urban runoff, and municipal and industrial wastewater. 

More than 97% of identified total mercury loading to the Delta/Yolo Bypass comes from tributary 

inputs; within-Delta sources are a very small component of overall loading. Losses include 

outflow to San Francisco Bay, water exports to southern California, removal of dredged 

sediments, and evasion. 

The Sacramento Basin, which is comprised of the Sacramento River and Yolo Bypass tributary 

watersheds, contributes 80% or more of total mercury fluxing through the Delta. Of the 

watersheds in the Sacramento Basin, the Cache Creek and upper Sacramento River (above 

Colusa) watersheds contribute the most mercury. The Cache Creek, Feather River, American 

River, and Putah Creek watersheds in the Sacramento Basin, and the Cosumnes River in the 

San Joaquin Basin, have both relatively large mercury loadings and high mercury 

concentrations in suspended sediment, which makes these watersheds attractive candidates for 

load reduction programs. 

Delta Methylmercury TMDL Report April 2010 iv
Methylmercury Allocations & Total Mercury Limits 

Methylmercury allocations were made in terms of the existing assimilative capacity of the 

different Delta subareas. To determine by how much methylmercury in ambient Delta waters 

needs to be reduced to achieve the proposed fish targets, the existing average methylmercury 

concentration in water in each Delta subarea was compared to the proposed methylmercury 

goal for ambient water (0.06 ng/l). The amount of reduction needed in each subarea is 

expressed as a percent of the ambient concentration. Percent reductions required in order to 

meet the goal ranged from 0% in the Central Delta subarea to about 80% in the Yolo Bypass 

and Mokelumne River subareas. 

In order to achieve the proposed fish targets in each Delta subarea, loads of methylmercury 

from within-Delta point and nonpoint sources and tributary inputs need to be reduced in 

proportion to the desired decrease in concentrations needed for ambient waters to meet the 

proposed goal. The percent reductions and allocations were calculated as percentages of 

existing loads. The percent reductions vary by subarea because the percent reductions 

required for ambient water methylmercury levels in each subarea to meet the proposed 

methylmercury goal vary. No reductions were recommended for sources to the Central and 

West Delta because the fish and water methylmercury levels achieve or almost achieve the 

proposed numeric targets and implementation goals, and because methylmercury levels are 

expected to decrease in these subareas as control actions take place upstream. Percent 

reductions were applied to point and nonpoint source loads within other subareas, except those 

sources that act as dilution (i.e., have existing average methylmercury concentrations at or 

below the proposed methylmercury goal of 0.06 ng/l). No individual point source would be 

expected to reduce its discharged methylmercury concentrations to below the proposed 

implementation goal (or, for nonpoint sources, below their intake water methylmercury 

concentrations). 

A total mercury load reduction strategy was developed to comply with the San Francisco Bay 

mercury control program, to maintain compliance with the USEPA’s criterion of 50 ng/l, and to 

help reduce aqueous methylmercury in the Delta. Staff applied the San Francisco Bay TMDL’s 

allocated reduction of 110 kg total mercury reduction to tributary inputs to the Delta/Yolo Bypass 

because within-Delta sources comprise only a couple percent of total mercury inputs. Initial 

mercury reduction efforts should focus on the watersheds that export the largest volume of 

highly contaminated sediment such as the Cache Creek, Feather River, American River, 

Cosumnes River, and Putah Creek watersheds. Chapter 4 of the draft Basin Plan Amendment 

staff report describes additional strategies for minimizing increases from total mercury sources. 

The methylmercury allocations and total mercury limits described in this report reflect the 

preferred implementation alternative described in Chapter 4 of the draft Basin Plan Amendment 

staff report and are designed to address the beneficial use impairment in all areas of the Delta 

and to comply with the total mercury allocation assigned by the San Francisco Bay TMDL. 

However, as described in the draft Basin Plan Amendment staff report, a number of alternatives 

are possible. The Central Valley Water Board will consider a variety of mercury reduction 

strategies and implementation alternatives as part of the Basin Plan amendment process. All 

Central Valley Water Board regulatory actions will be taken during public hearings. 

Delta Methylmercury TMDL Report v April 2010 
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Delta Methylmercury TMDL Report vi April 2010 
SACRAMENTO – SAN JOAQUIN DELTA ESTUARY TMDL FOR METHYLMERCURY 

Staff Report 

TABLE OF CONTENTS 

Executive Summary.....................................................................................................................i

Table of Contents......................................................................................................................vii

Acronyms .................................................................................................................................xvi

Units of Measure ....................................................................................................................xviii

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

2 Problem Statement.................................................................................................................5

2.1 Regulatory Background & TMDL Timeline.....................................................................5

2.1.1 Clean Water Act 303(d) Listing and Total Maximum Daily Load Development..5

2.1.2 Porter-Cologne Basin Plan Amendment Process...............................................5

2.1.3 Timeline and Process for the Delta Mercury Management Strategy ..................6

2.1.4 Units and Terms Used in this Report..................................................................7

2.2 Delta Characteristics and TMDL Scope .........................................................................8

2.2.1 Delta Geography ................................................................................................8

2.2.2 TMDL Scope & Delta Subareas .......................................................................12

2.3 Mercury Effects & Sources...........................................................................................14

2.3.1 Mercury Chemistry and Accumulation in Biota.................................................14

2.3.2 Toxicity of Mercury ...........................................................................................15

2.3.3 Mercury Sources & Historic Mining Activities ...................................................15

2.4 Beneficial Uses, Applicable Standards & Extent of Impairment...................................17

2.4.1 Sacramento-San Joaquin Delta Estuary Beneficial Uses.................................17

2.4.2 Applicable Standards & Extent of Impairment..................................................18

Key Points............................................................................................................................22

3 Potentially Controllable Methylation Processes in the Delta ...........................................23

3.1 Sulfate ..........................................................................................................................24

3.2 New Water Impoundments...........................................................................................25

3.3 Sediment Mercury Concentrations ...............................................................................26

3.4 Forms of Mercury .........................................................................................................29

3.5 Wetlands ......................................................................................................................29

3.6 Methylmercury Loss by Sedimentation and Photodemethylation.................................31

Key Points............................................................................................................................32

Delta Methylmercury TMDL Report vii April 2010 
4 Numeric Targets ...................................................................................................................33

4.1 Definition of a Numeric Target......................................................................................33

4.2 Clean Water Act 303(d) Listing and Beneficial Use Impairment ..................................33

4.3 Selection of the Type of Target for the Delta................................................................34

4.3.1 Fish Tissue .......................................................................................................34

4.3.2 San Francisco Bay Numeric Target..................................................................34

4.3.3 Water Criteria ...................................................................................................35

4.4 Fish Tissue Target Equation and Development ...........................................................35

4.5 Wildlife Health Targets .................................................................................................36

4.5.1 Reference Doses, Body Weights & Consumption Rates..................................37

4.5.2 Safe Methylmercury Levels in Total Diet ..........................................................37

4.5.3 Calculation of Safe Fish Tissue Levels from Total Diet Values ........................40

4.6 Human Health Targets .................................................................................................45

4.6.1 Acceptable Daily Intake Level ..........................................................................45

4.6.2 Body Weight & Consumption Rate...................................................................45

4.6.3 Consumption of Fish from Various Trophic Levels & Sources .........................47

4.6.4 Safe Rates of Consumption of Delta Fish ........................................................48

4.7 Trophic Level Food Group Evaluation..........................................................................52

4.7.1 Data Used in Trophic Level Food Group Evaluation ........................................52

4.7.2 Trophic Level Food Group Comparisons..........................................................53

4.8 Largemouth Bass Evaluation .......................................................................................58

4.8.1 Largemouth Bass Standardization ...................................................................59

4.8.2 Correlations between Standard 350 mm and All Largemouth Bass Data ........59

4.8.3 Largemouth Bass/Trophic Level Food Group Comparisons ............................59

Key Points............................................................................................................................64

Options to Consider .............................................................................................................65

5 Linkage Analysis ..................................................................................................................67

5.1 Data Used in Linkage Analysis ....................................................................................67

5.2 Bass/Water Methylmercury Regressions & Calculation of Aqueous 

Methylmercury Goal .....................................................................................................70

5.3 Evaluation of a Filtered Aqueous Methylmercury Linkage Analysis.............................74

Key Points............................................................................................................................75

6 Source Assessment – Methylmercury................................................................................77

6.1 Water Budget ...............................................................................................................78

6.2 Methylmercury Sources................................................................................................78

6.2.1 Tributary Inputs.................................................................................................81

6.2.2 Within-Delta Sediment Flux..............................................................................88

6.2.3 Municipal & Industrial Sources .........................................................................92

6.2.4 Agricultural Return Flows ...............................................................................104

6.2.5 Urban Runoff ..................................................................................................108

6.2.6 Atmospheric Deposition..................................................................................114

6.2.7 Other Potential Sources .................................................................................115

Delta Methylmercury TMDL Report viii April 2010 
6.3 Methylmercury Losses ...............................................................................................117

6.3.1 Outflow to San Francisco Bay ........................................................................118

6.3.2 South of Delta Exports....................................................................................118

6.3.3 Export via Dredging........................................................................................119

6.3.4 Other Potential Loss Pathways ......................................................................120

6.4 Delta Methylmercury Mass Budget & East-West Concentration Gradient .................125

Key Points..........................................................................................................................129

7 Source Assessment – Total Mercury & Suspended Sediment.......................................131

7.1 Total Mercury and Suspended Sediment Sources.....................................................131

7.1.1 Tributary Inputs...............................................................................................132

7.1.2 Municipal & Industrial Sources .......................................................................146

7.1.3 Urban Runoff ..................................................................................................147

7.1.4 Atmospheric Deposition..................................................................................150

7.1.5 Other Potential Sources .................................................................................154

7.2 Total Mercury and TSS Losses..................................................................................155

7.2.1 Outflow to San Francisco Bay ........................................................................155

7.2.2 Exports South of Delta....................................................................................157

7.2.3 Dredging.........................................................................................................158

7.2.4 Evasion...........................................................................................................159

7.3 Total Mercury & Suspended Sediment Budgets ........................................................159

7.4 Evaluation of Suspended Sediment Mercury Concentrations & CTR Compliance ....160

7.4.1 Suspended Sediment Mercury Concentrations ..............................................160

7.4.2 Compliance with the USEPA’s CTR...............................................................164

Key Points..........................................................................................................................169

8 Methylmercury Allocations, Total Mercury Limits & Margin of Safety ..........................171

8.1 Methylmercury Load Allocations ................................................................................171

8.1.1 Definition of Assimilative Capacity..................................................................172

8.1.2 Allocation Strategy..........................................................................................176

8.1.3 Calculation Methods for NPDES Facility Waste Load Allocations..................178

8.1.4 Percent Allocation Calculations......................................................................186

8.2 Total Mercury Load Reduction Requirement for Tributary Watersheds .....................196

8.3 Margin of Safety .........................................................................................................202

8.4 Seasonal & Inter-annual Variability ............................................................................202

8.4.1 Variability in Aqueous Methyl and Total Mercury ...........................................202

8.4.2 Variability in Biota Mercury .............................................................................203

8.4.3 Regional and Global Change .........................................................................203

Key Points..........................................................................................................................211

Options to Consider ...........................................................................................................212

9 References ..........................................................................................................................213

Delta Methylmercury TMDL Report April 2010 ix
LIST OF APPENDICES 

A. Waterways within the Sacramento-San Joaquin Delta 

B. Summary of Fish Mercury Data Used in TMDL Numeric Target and Linkage Analysis 

Calculations 

C. Commercial and Sport Fishing in the Sacramento-San Joaquin Delta 

D. Available Aqueous Methylmercury Data and Pooled Values Used in Delta Linkage 

E. Methods Used to Estimate Water Volumes for Delta and Sacramento Basin Inputs 

and Exports 

F. Summary of Methylmercury Concentration Data for Major Delta Tributary Input and 

Export Loads 

G. Information about NPDES-Permitted Facilities in the Delta and Its Tributary Watersheds 

H. Urban Runoff Constituent Concentration Data 

I. Summary of Total Mercury and TSS Concentration Data for Major Delta Tributary Input and 

Export Loads 

J. 2002 Annual Total Mercury Loads from Air Emission Facilities that Reported to the 

California Air Resources Board 

K. Fish Mercury Concentration Data Incorporated in TMDL Report 

L. Aqueous Methylmercury, Total Mercury and TSS Concentration Data Incorporated in 

TMDL Report 

Delta Methylmercury TMDL Report x April 2010 
LIST OF TABLES 

Table 2.1: Spatial Perspective of the Delta and Its Source Regions.......................................... 11

Table 2.2: Key Delta Features ................................................................................................... 11

Table 2.3: Beneficial Uses of the Delta and Yolo Bypass .......................................................... 18

Table 3.1: Field Studies Demonstrating a Positive Correlation Between Total Mercury and 

Methylmercury in Freshwater Surficial Sediment...................................................... 27

Table 3.2: Change in Fish Tissue Mercury Concentration After Initiation of Source Control. .... 28

Table 3.3: Summary of Wetland Methylmercury Production Characteristics. ............................ 30

Table 4.1: Exposure Parameters for Fish-Eating Wildlife .......................................................... 38

Table 4.2: Concentrations of Methylmercury in Total Diet to Protect Delta Wildlife Species ..... 39

Table 4.3: Safe Concentrations of Methylmercury in Fish (mg/kg) by Trophic Level to 

Protect Wildlife .......................................................................................................... 40

Table 4.4: Food Chain Multipliers and Trophic Level Ratios for Delta Wildlife Target 

Development............................................................................................................. 42

Table 4.5: Safe Concentrations of Methylmercury in Delta Fish by Trophic Level (TL) to 

Protect Humans Calculated Using Varying Assumptions about Consumption 

Rates and Trophic Level Distribution. ....................................................................... 51

Table 4.6: Trophic Level Ratios for Delta Human Target Development..................................... 52

Table 4.7: Mercury Concentrations in Trophic Level Food Groups Sampled in the Delta ......... 54

Table 4.8: Percent Reductions in Fish Methylmercury Levels Needed to Meet 

Numeric Targets........................................................................................................ 54

Table 4.9: Predicted Safe Concentrations of Methylmercury in 150-500 mm TL4 Fish and 

Standard 350-mm Largemouth Bass Corresponding to Trophic Level Food 

Group (TLFG) Targets for the Protection of Piscivorous Species............................. 55

Table 4.10: Mercury Concentrations in Standard 350-mm and 300-400 mm Largemouth Bass . 60

Table 4.11: Percent Reductions in Standard 350-mm Largemouth Bass Methylmercury Levels 

Needed to Meet the Recommended Implementation Goal of 0.24 mg/kg in Each 

Delta Subarea. .......................................................................................................... 60

Table 5.1: Fish and Water Methylmercury Values by Delta Subarea. ....................................... 68

Table 5.2: Relationships between Methylmercury Concentrations in Water and Standard 

350-mm Largemouth Bass........................................................................................ 73

Table 5.3. Ambient Water Methylmercury Concentrations that Correspond to Alternative 

Fish Tissue Objectives Evaluated in the Basin Plan Amendment Staff Report. ....... 74

Table 5.4: Average and Median Filtered Methylmercury Concentrations (ng/l) for March 2000 

to October 2000 for Each Delta Subarea.................................................................. 75

Table 6.1: Average Annual Water Volumes for Delta/Yolo Bypass Inputs and Losses ............. 79

Table 6.2: Methylmercury Concentrations and Loads to the Delta/Yolo Bypass for 

WY2000-2003. .......................................................................................................... 80

Table 6.3: Methylmercury Concentrations for Tributary Inputs. ................................................. 86

Table 6.4: Methylmercury Loading from Wetland and Open Water Habitats in Each Delta 

Subarea..................................................................................................................... 91

Delta Methylmercury TMDL Report xi April 2010 
Table 6.5: Summary of Unfiltered Methylmercury Concentration Data for Effluent from 

NPDES-permitted Facilities That Discharged to the Delta and Yolo Bypass North 

of the Delta during the WY2000-2003 Period and Later. .......................................... 94

Table 6.6: Values Used to Estimate MeHg Loads from Agricultural Lands within the Legal 

Delta Boundary ....................................................................................................... 107

Table 6.7: Delta Agricultural Main Drain Methylmercury Concentration Data.......................... 107

Table 6.8: Delta-wide Island Consumptive Use Estimates – Water Year 1999 ....................... 107

Table 6.9: Agricultural Acreage and Methylmercury Load Estimates by Delta Subarea.......... 108

Table 6.10: Urban Acreage and MS4 Permits that Regulate Urban Runoff within the 

Delta/Yolo Bypass................................................................................................... 110

Table 6.11: Summary of Urban Runoff Methylmercury Concentrations..................................... 113

Table 6.12: Average Annual Methylmercury Loading from Urban Areas within Each Delta 

Subarea for WY2000-2003 ..................................................................................... 113

Table 6.13: Comparison of Sacramento and Stockton Area MS4 Methylmercury Loading to 

Delta Methylmercury Loading for WY2000-2003. ................................................... 114

Table 6.14: Estimate of Average Annual Methylmercury Loading from Wet Deposition............ 115

Table 6.15: Methylmercury Concentrations and Loads Lost from the Delta for WY2000-2003. 117

Table 6.16: Methylmercury Concentrations for the Delta’s Major Exports ................................. 121

Table 6.17: Recent Dredge Projects within the Delta. ............................................................... 124

Table 6.18: MeHg:TotHg in Deep Water Ship Channel Surficial Sediments ............................. 125

Table 7.1: Average Annual Total Mercury and TSS Source Loads for WY2000-2003 and 

WY1984-2003. ........................................................................................................ 132

Table 7.2: Total Mercury and TSS Concentrations for Tributary Inputs................................... 135

Table 7.3: Comparison of Load Estimates for Sacramento Basin Discharges to the Delta ..... 136

Table 7.4: Comparison of Loading Estimates for Other Major Delta Tributaries...................... 139

Table 7.5: Total Mercury and TSS Concentrations for Sacramento Basin Tributaries. ........... 143

Table 7.6a: Sacramento Basin Tributaries – Acreage and Water Volumes............................... 144

Table 7.6b: Sacramento Basin Tributaries – Total Mercury Loads. ........................................... 144

Table 7.6c: Sacramento Basin Tributaries – TSS Loads........................................................... 145

Table 7.7: Summary of Urban Runoff Total Mercury and TSS Concentrations ....................... 148

Table 7.8: Average Annual Total Mercury and TSS Loadings from Urban Areas within the 

Delta/Yolo Bypass................................................................................................... 149

Table 7.9: Comparison of WY1984-2003 Annual Delta Mercury and TSS Loads to 

Sacramento and Stockton Area MS4 Loads. .......................................................... 149

Table 7.10: Summary of Available Data Describing Mercury Concentrations in Wet Deposition 

in Northern and Central California........................................................................... 151

Table 7.11: Average Annual Total Mercury Loads from Wet Deposition ................................... 152

Table 7.12: Average Annual Total Mercury and TSS Losses for WY2000-2003 and 

WY1984-2003. ........................................................................................................ 155

Table 7.13: Summary of Total Mercury and TSS Concentration Data for X2 ............................ 156

Table 7.14: Estimates of Delta Exports to San Francisco Bay................................................... 157

Table 7.15: Summary of Total Mercury and TSS Concentration Data for Exports South of 

the Delta.................................................................................................................. 158

Delta Methylmercury TMDL Report xii April 2010 
Table 7.16: Water, Total Mercury and TSS Budgets for the Delta for WY2000-2003 and 

WY1984-2003. ........................................................................................................ 160

Table 7.17: Mercury to Suspended Sediment Ratios for Delta Inputs and Exports ................... 163

Table 7.18: Evaluation of CTR Compliance at Delta and Sacramento Basin Tributary 

Locations................................................................................................................. 168

Table 8.1: Aqueous Methylmercury Reductions Needed to Meet the Proposed 

Methylmercury Goal of 0.06 ng/l. ............................................................................ 175

Table 8.2: Assimilative Capacity Calculations for Each Delta Subarea. .................................. 175

Table 8.3a: Total Existing Municipal WWTP Effluent Volume Discharged to Each Delta Subarea, 

Predicted Increases Due to Population Growth, and Volumes and Methylmercury 

Loads Predicted to Be Discharged by New WWTPs. ............................................. 185

Table 8.3b: Predicted Effluent Volumes Used to Calculate Corresponding Methylmercury 

Loads for Municipal WWTPs that Discharge Effluent with Average Methylmercury 

Concentrations Less than 0.06 ng/l......................................................................... 186

Table 8.4a: Allocations for Methylmercury Sources to the Central Delta Subarea .................... 189

Table 8.4b: Allocations for Methylmercury Sources to the Marsh Creek Subarea..................... 190

Table 8.4c: Allocations for Methylmercury Sources to the Mokelumne River Subarea ............. 190

Table 8.4d: Allocations for Methylmercury Sources to the Sacramento River Subarea ............ 191

Table 8.4e: Allocations for Methylmercury Sources to the San Joaquin River Subarea............ 192

Table 8.4f: Allocations for Methylmercury Sources to the West Delta Subarea........................ 193

Table 8.4g: Allocations for Methylmercury Sources to the Yolo Bypass Subarea ..................... 194

Table 8.5: Methylmercury Load and Waste load Allocations for Each Delta Subarea by 

Source Category ..................................................................................................... 195

Table 8.5: Preliminary Evaluation of Potential Watershed Total Mercury Load Reductions...... 201

Delta Methylmercury TMDL Report xiii April 2010 
LIST OF FIGURES 

Figure 1.1: The Sacramento-San Joaquin Delta. .......................................................................4

Figure 2.1: The Central Valley..................................................................................................10

Figure 2.2: Hydrology-Based Delineation of Subareas within the Legal Delta and 

Yolo Bypass ...........................................................................................................13

Figure 4.1: Fish and Water Sampling Locations Included in the Trophic Level Food Group 

and Largemouth Bass Evaluations.........................................................................56

Figure 4.2: Comparison of Methylmercury Concentrations in Large (150-500 mm) TL4 Fish 

and Other Trophic Level (TL) Food Groups. ..........................................................57

Figure 4.3: Site-specific Relationship between Largemouth Bass Length and Mercury 

Concentrations in the Delta. ...................................................................................61

Figure 4.4: Comparison of Mercury Levels in Standard 350 mm Largemouth Bass (LMB) 

Collected at Linkage Sites in 2000 and Mercury Levels in 300-400 mm LMB 

Collected throughout Each Subarea in 1998-2000. ...............................................62

 Figure 4.5: Comparison of Mercury Concentrations in Standard 350-mm Largemouth Bass 

(LMB) Caught in September/October 2000 and Composites of Fish from Various 

Trophic Level (TL) Food Groups Caught between 1998 and 2001. .......................63

Figure 5.1: Aqueous and Largemouth Bass Methylmercury Sampling Locations Used in the 

Linkage Analysis. ...................................................................................................69

Figure 5.2: Relationships between Standard 350-mm Largemouth Bass Methylmercury and 

March to October 2000 Unfiltered Aqueous Methylmercury...................................73

Figure 5.3: Relationships between Standard 350-mm Largemouth Bass Mercury Levels and 

March to October 2000 Filtered Aqueous Methylmercury......................................75

Figure 6.1: Watersheds that Drain to the Delta and Yolo Bypass. ...........................................84

Figure 6.2: Tributary Aqueous Methylmercury Monitoring Locations .......................................85

Figure 6.3a: Methylmercury Concentrations for Major Tributary Inputs......................................87

Figure 6.3b: Methylmercury Concentrations for Small Tributary Inputs......................................88

Figure 6.4: Delta and Yolo Bypass Wetlands and Open Water Habitat. ..................................90

Figure 6.5: NPDES Facilities that Discharge to the Statutory Delta and Yolo Bypass. ............93

Figure 6.6: City of Stockton WWTP Effluent Ammonia, Methylmercury, and Total Mercury 

Concentration Data Collected Before and After WWTP Upgrades ......................102

Figure 6.7: Agricultural Lands within the Statutory Delta Boundary and Yolo Bypass. ..........106

Figure 6.8: NPDES Permitted Municipal Separate Storm Sewer System (MS4) Areas in the 

Delta Region.........................................................................................................111

Figure 6.9: Urban Areas and Aqueous MeHg Sampling Locations in the Delta Region. .......112

Figure 6.10: Aqueous Monitoring Locations for Major Methylmercury Exports and 

Approximate Locations of Recent Dredging Projects...........................................122

Figure 6.11: Available Methylmercury Concentration Data for the Delta’s Major Exports ........123

Figure 6.12: Average Daily Delta/Yolo Bypass Methylmercury Inputs and Exports. ................127

Delta Methylmercury TMDL Report xiv April 2010 
Figure 6.13: Water Sampling Transects down the Sacramento River to Ascertain Location 

of Methylmercury Concentration Decrease. .........................................................128

Figure 7.1: Sacramento River Flood Control System. ............................................................142

Figure 7.2: Flow Data Evaluated for Sutter Bypass................................................................145

Figure 7.3: Wet Deposition Total Mercury Sampling Locations in Northern and Central 

California. .............................................................................................................153

Figure 7.4: Grab Sample and Regression-Based 30-Day Running Average Total Mercury 

Concentrations for Delta Locations with Statistically Significant (P<0.05) 

Aqueous TotHg/Flow Correlations .......................................................................166

 Figure 7.5: Grab Sample and Regression-Based 30-Day Running Average Total Mercury 

Concentrations for Sacramento Basin Tributary Locations with Statistically 

Significant (P<0.05) Aqueous TotHg/Flow Correlations .......................................167

Delta Methylmercury TMDL Report xv April 2010 
ACRONYMS 

§ Section 

ARB California Air Resources Board 

AWQC Ambient water quality criterion 

BAF Bioaccumulation factor 

Basin Plan Central Valley Region Water Quality Control Plan for the Sacramento River and 

San Joaquin River Basins 

bwt Body weight 

CCSB Cache Creek Settling Basin 

CDEC California Data Exchange Center 

CDFG California Department of Fish and Game 

CDHS California Department of Health Services, re-organized in 2007 and renamed 

“California Department of Health” (CDPH). Reports issued before the 2007 

re-organization are cited as “CDHS” reports. 

CDPH California Department of Health 

CEIDARS California emission inventory department and reporting system 

cfs Cubic feet per second 

CFSII Continuing survey of food intake by individuals 

CMP Coordinated Monitoring Program 

CSS Combined Sewer system 

CTR California Toxics Rule 

CVP Central Valley Project 

CVRWQCB Central Valley Regional Water Quality Control Board 

(a.k.a. Central Valley Water Board) 

CWA Federal Clean Water Act 

df Degrees of freedom (for statistical analyses) 

DMC Delta Mendota Canal 

DTMC Delta Tributaries Mercury Council 

DWR California Department of Water Resources 

EC Electrical conductivity 

FCM Food chain multipliers 

GIS Geographic Information System 

HCI Hydrologic Classification Index 

Hg Mercury 

IEP Interagency Ecological Program 

IRIS Integrated Risk Information System 

LMB Largemouth bass 

LOAEC’s Lowest observed adverse effect concentrations 

MCL California/USEPA drinking water standards maximum contaminant levels 

MDN Mercury Deposition Network 

mgd Million gallons per day 

MeHg Monomethyl mercury (also referred to as methylmercury in this report) 

MS4 Municipal Separate Storm Sewer System 

Delta Methylmercury TMDL Report xvi April 2010 
ACRONYMS, continued

NA Not applicable 

NADP National Atmospheric Deposition Program 

NAS National Academy of Sciences 

NEMD Natomas East Main Drain 

NPDES National Pollutant Discharge Elimination System 

NPS Nonpoint source 

NWI National Wetland Inventory 

O Oxygen 

o/oo Parts per thousand (salinity) 

OBS Optical back scatter 

OEHHA Office of Environmental Health Hazard Assessment 

RFD Reference dose 

RSC Relative source contribution 

San Francisco 

Water Board 

San Francisco Bay Regional Water Quality Control Board 

SFBADPS San Francisco Bay Atmospheric Deposition Pilot Study 

SFEI San Francisco Estuary Institute 

SRCSD Sacramento Regional County Sanitation District 

SRWP Sacramento River Watershed Program 

State Board State Water Resources Control Board (also shown as SWRCB in reference citations) 

Subwatershed Portion of watershed that is either upstream or downstream of the most-downstream 

major dam 

SWIM Surface water information 

SWP State water project 

SWRCB State Water Resources Control Board 

TDSL Total diet safe level 

TL Trophic level 

TLR Trophic level ratios 

TMDL Total Maximum Daily Load 

TSS Total suspended solids 

USACE U.S. Army Corps of Engineers 

USBR U.S. Bureau of Reclamation 

USEPA U.S. Environmental Protection Agency 

USFDA U.S. Food and Drug Administration. 

USFWS U.S. Fish and Wildlife Service 

USGS U.S. Geological Survey 

ww Wet weight concentration (e.g., for fish tissue mercury concentrations) 

WWTP Wastewater treatment plants 

X2 Location in the Estuary with 2-o/oo bottom salinity 

Delta Methylmercury TMDL Report xvii April 2010 
Delta Methylmercury TMDL Report xviii April 2010 

UNITS OF MEASURE 

μg microgram 

μg/g microgram per gram 

μg/l microgram per liter 

μm micrometer 

cfs cubic feet per second

cm centimeter 

g Gram 

g/day gram per day 

g/l gram per liter 

in/yr inches per year 

kg kilogram 

l liter 

m meter 

mg milligram 

mg/g milligram per gram 

ml milliliter 

mm millimeter 

ng nanograms 

ng/l nanograms per liter 

o/oo parts per thousand 

(salinity) 

ppb parts per billion; 

usually μg/kg 

ppm parts per million; 

usually mg/kg or μg/g

ppt parts per trillion; 

usually ng/kg 

 
1 INTRODUCTION 

This draft report presents Central Valley Regional Water Quality Control Board (Central Valley 

Water Board) staff recommendations for establishing a Total Maximum Daily Load for 

methylmercury in the Sacramento-San Joaquin Delta Estuary (Figure 1.1). The report contains 

an analysis of the mercury impairment, a discussion of the primary sources, a linkage between 

sources and impairments, and recommended methyl and total mercury reductions to eliminate 

the impairment. The report is one component in the Central Valley Water Board’s water quality 

attainment strategy to resolve the mercury impairment in the Delta. 

The Federal Clean Water Act (CWA) requires states to identify water bodies that do not meet 

their designated beneficial uses and to develop programs to eliminate impairments. States refer 

to the control program as a Total Maximum Daily Load (TMDL) program. A TMDL is the total 

maximum daily load of a pollutant that a water body can assimilate and still attain beneficial 

uses. The Central Valley Water Board determined in 1990 that the Delta was impaired because 

fish had elevated levels of mercury that posed a risk for human and wildlife consumers. In 

addition, the San Francisco Bay Regional Water Quality Control Board (San Francisco Bay 

Water Board) identified Central Valley outflows via the Delta as one of the principal sources of 

total mercury to San Francisco Bay and assigned the Central Valley a load reduction (Johnson 

and Looker, 2004; SFBRWQCB, 2006). Therefore, the final mercury TMDL control plan for the 

Delta must ensure protection of human and wildlife health in the Delta and meet the San 

Francisco Bay Water Board’s mercury load allocation to the Central Valley. 

In order to meet state and federal requirements, the TMDL development process must include 

compiling and considering available information and appropriate analyses relevant to defining 

the impairment, identifying sources, and assigning responsibility for actions to resolve the 

impairment. This report has the following sections that reflect the key elements of the Delta 

methylmercury TMDL development process: 

• Chapter 2 – Problem Statement: Presents information that explains the overall regulatory 

framework for this TMDL, lists future milestones and describes the extent of mercury 

impairment in the Delta. 

• Chapter 3 – Controllable Processes: Describes the methylation processes that are 

potentially controllable in the Delta. The concepts summarized in this chapter guided the 

development of the methylmercury TMDL for the Delta, particularly the linkage analyses 

(Chapter 5), methyl and total mercury source analyses (Chapters 6 and 7), and 

methylmercury allocation and implementation strategies described in Chapter 4 of the 

draft Basin Plan Amendment staff report. 

• Chapter 4 – Numeric Targets: Proposes numeric targets for methylmercury 

concentrations in fish, which, if met, would protect beneficial uses of Delta waters. 

• Chapter 5 – Linkage Analysis: Describes the mathematical relationship between aqueous 

methylmercury concentrations and the proposed numeric targets for fish mercury levels, 

which is used to determine an aqueous methylmercury goal that guides the allocation of 

methylmercury source reductions within the statutory Delta boundary and tributary inputs. 

• Chapters 6 & 7 – Source Assessment: Identifies and quantifies concentrations and loads 

of methyl and total mercury sources. 

Delta Methylmercury TMDL Report 1 April 2010 
• Chapter 8 – Allocations: Presents recommended methylmercury allocations and total 

mercury limits for Delta sources to reduce methylmercury concentrations in fish and to 

comply with the USEPA’s California Toxics Rule mercury criterion and the San Francisco 

Bay Mercury TMDL allocation for total mercury leaving the Central Valley watershed. 

This chapter also describes the margin of safety afforded by the analyses’ uncertainties 

and consideration of seasonal variations. 

Since the June 2006 draft TMDL Report issued for scientific peer review, staff made several 

changes to the TMDL Report in response to comments made by the scientific peer reviewers 

and other agencies and stakeholders, as reflected in the February 2008 draft TMDL Report: 

• Expansion of the numeric target evaluation (Chapter 4) to include results from recent 

interviews of local community-based groups and pilot surveys and recent final and draft 

fish mercury advisories for the Delta region. 

• Expansion of the methylmercury source analysis (Chapter 6) and methylmercury 

allocation scheme (Chapter 8) to include methylmercury inputs to the portion of the Yolo 

Bypass that is north of the legal Delta using methods evaluated and found acceptable by 

the scientific peer reviewers. About 72% of the 73,300-acre Yolo Bypass is within the 

legal Delta boundary. Previous analyses indicated that the Yolo Bypass is a substantial 

source of methylmercury to the Delta, such that it makes sense to expand the 

methylmercury allocation scheme for the legal Delta to include the northern Yolo Bypass. 

Sacramento and Feather Rivers (via Fremont and Sacramento Weirs), Cache Creek, 

Willow Slough, and the Knights Landing Ridge Cut from the Colusa Basin all drain 

directly to the Yolo Bypass north of the legal Delta. Sources within the northern Yolo 

Bypass include wetlands and open water habitats, two WWTP discharges, agricultural 

lands, and a small amount of urbanized land. The 2006 draft TMDL Report included 

methylmercury allocations for sources within 30 miles of the legal Delta boundary; this 

revised report only includes allocations for dischargers within the legal Delta and the Yolo 

Bypass. 

• Additional explanation of, and calculations for, the proposed methylmercury allocations to 

more directly address expected increases in source loading from predicted population 

growth and wetland restoration efforts. 

• Changes to the methylmercury allocation strategy such that point and nonpoint sources 

with load-based allocations do not also have concentration allocations; this allows for a 

greater range of implementation options. 

• Re-evaluation of the wetland and open-water methylmercury contributions (Chapter 6) 

using 2006 National Wetlands Inventory (NWI) wetland and open water acreages for the 

Delta/Yolo Bypass rather than the 1997 NWI acreages. 

• Minor changes to methylmercury, total mercury and TSS load calculations (Chapters 6 

and 7) based on additional quality assurance review of the concentration data and their 

use in regression-based load analyses. 

• Minor textual changes throughout the report to clarify concepts and correct typographical 

errors identified in the June 2006 report. 

• Expansion and re-location of the “Public Outreach” chapter (Chapter 9 in the June 2006 

TMDL report) to the draft Basin Plan Amendment staff report (Chapter 8, “Public 

Participation & Agency Consultation”). 

Delta Methylmercury TMDL Report 2 April 2010 
Since the February 2008 draft TMDL Report issued for public review, staff made several more 

changes to the TMDL Report in response to comments made by stakeholders, as reflected in 

this revised draft TMDL Report: 

• Changes to the methylmercury allocation strategy so that NPDES facilities have more 

implementation options to address future population growth, regionalization, and 

reclamation. 

• Minor modifications to methylmercury and total mercury load calculations (Chapters 6 

and 7) based on (a) new inputs from NPDES facilities that previously did not discharge to 

surface water, (b) decreases because some NPDES facilities have ceased their 

discharges to surface water, (c) new discharge data for NPDES facilities for which 

previously no data were available; and (d) additional quality assurance review of the 

tributary inputs and NPDES facility concentration data and their use in load analyses. 

• Addition of new information from recently completed CalFed mercury science reports and 

other recent published literature. 

• Minor textual changes throughout the report to clarify concepts and correct typographical 

errors identified in the February 2008 report. 

Staff reviewed key mercury studies in the Delta and elsewhere that have been published since 

the Delta methylmercury TMDL was drafted. These studies include the 2008 CALFED Bay 

Delta Program mercury studies and atmospheric deposition and wetland methylmercury loading 

research. Several of these studies are cited in Chapters 3, 6, and 7. Others have been 

discussed in stakeholder meetings. Staff concluded that recent information does not 

necessitate changes in the Delta TMDL at this time and generally supports a phased 

implementation strategy that includes development of methylmercury management measures, 

production of upstream TMDLs to address methylmercury and inorganic mercury sources, and 

methylmercury reductions for sources within the Delta. Staff will use studies published after the 

TMDL was developed to revise methylmercury and mercury load calculations and 

implementation strategy when the Delta methylmercury control program is reviewed at the end 

of Phase 1. 

Delta Methylmercury TMDL Report 3 April 2010 
Figure 1.1: The Sacramento-San Joaquin Delta [DWR, 1995]. 

The dotted red line outlines the statutory boundary of the Delta. 

Delta Methylmercury TMDL Report 4 April 2010 
2 PROBLEM STATEMENT 

The Central Valley Water Board determined that the Delta is impaired by mercury. Fish tissue 

data collected since 1970 in the Delta indicate that mercury levels exceed numeric criteria 

established for the protection of human and wildlife health. This Problem Statement presents 

information in four sections: 

1. Regulatory Background and TMDL Timeline 

2. Delta Characteristics and TMDL Scope 

3. Mercury Effects & Sources 

4. Beneficial Uses, Applicable Standards & Extent of Impairment 

2.1 Regulatory Background & TMDL Timeline 

2.1.1 Clean Water Act 303(d) Listing and Total Maximum Daily Load Development 

Section 303(d) of the federal Clean Water Act requires states to: 

• Identify waters not attaining water quality standards (referred to as the “303(d) list”). 

• Set priorities for addressing the identified pollution problems. 

• Establish a “Total Maximum Daily Load” for each identified water body and pollutant to 

attain water quality standards. 

In 1990 the State Water Resources Control Board (State Water Board) adopted the 303(d) List 

that identified Delta waterways as impaired for mercury because of the presence of a fish 

consumption advisory (SWRCB-DWQ, 1990). The 1998 303(d) List identified the TMDL control 

program for mercury in the Delta as a high priority (SWRCB-DWQ, 2003). 

A TMDL represents the maximum load (usually expressed as a rate, such as kilograms per day 

(kg/day) or other appropriate measure) of a pollutant that a water body can receive and still 

meet water quality objectives. A TMDL describes the reductions needed to meet water quality 

objectives and allocates those reductions among the sources in the watershed. Water bodies 

on the 303(d) List are not expected to meet water quality objectives even if point source 

dischargers comply with their current discharge permit requirements. TMDLs must include the 

following elements: description of the problem (Chapter 2), numerical water quality target 

(Chapter 4), analysis of current loads (Chapters 6 and 7), and load reductions needed to 

eliminate impairments (Chapter 8). 

2.1.2 Porter-Cologne Basin Plan Amendment Process 

The State of California Porter-Cologne Water Quality Control Act (Section 13240) requires the 

Central Valley Water Board to develop a water quality control plan for each water body in the 

Central Valley that does not meet its designated beneficial uses. The Water Quality Control 

Plan for the Sacramento River and San Joaquin River Basins (the Basin Plan) is the legal 

document that describes the beneficial uses of all water bodies in these basins, water quality 

objectives to protect them, and, if the objectives are not being met, an implementation program 

Delta Methylmercury TMDL Report 5 April 2010 
to correct the impairment (CVRWQCB, 2009). The water quality management strategy for 

mercury in the Delta includes: 

• TMDL Development: involves the technical analysis of methyl and total mercury sources, 

fate and transport of each, development of proposed mercury fish tissue objectives, and a 

description of the amount of source reduction necessary to attain the proposed 

objectives. 

• Basin Planning: focuses on the development of Basin Plan amendments and a staff 

report for Central Valley Water Board consideration. The draft Basin Plan amendments 

propose site-specific fish tissue objectives for the Delta and an implementation plan to 

achieve the objectives. The draft Basin Plan Amendment staff report includes information 

and analyses required to comply with the California Environmental Quality Act (CEQA). 

The Basin Planning process satisfies State Water Board regulations for the 

implementation of CEQA.2

 

• Implementation: focuses on the establishment of a framework that ensures that 

appropriate practices or technologies are implemented (§13241 and §13242 of the 

Porter-Cologne Water Quality Act), including those elements necessary to meet federal 

TMDL requirements (CWA Section 303(d)). 

The proposed Basin Plan amendments are legally enforceable once they have been adopted by 

the Central Valley and State Water Boards and approved by the Office of Administrative Law 

and the USEPA. Central Valley Water Board staff solicited public participation and scientific 

review throughout the TMDL development and implementation planning phases. Chapter 8 in 

the draft Basin Plan Amendment staff report describes the extensive public participation, 

scientific peer review, and agency consultation that have taken place to date. Also, the Basin 

Plan amendments will be adopted and approved in a public forum. 

2.1.3 Timeline and Process for the Delta Mercury Management Strategy 

The Delta methylmercury TMDL and Basin Planning processes began with the development of 

a draft technical mercury TMDL report, which was submitted to the USEPA in August 2005 and 

posted on the Central Valley Water Board website for public review. The June 2006 TMDL 

Report incorporated additional information from ongoing sampling and analyses and public input 

received on the August 2005 draft TMDL report. The February 2008 draft TMDL report 

addressed scientific peer review comments and considered Central Valley Water Board 

member comments and questions voiced during the March 2007 workshop, additional input 

from agencies and other stakeholders, and supplementary evaluations to support the Basin 

Planning effort. This draft TMDL Report, along with the accompanying draft Basin Plan 

Amendment staff report and formal responses to comments under separate cover, addresses 

Central Valley Water Board member and stakeholder comments voiced during the April 2008 

hearing and 2008-2009 Stakeholder Process. Chapter 8 in the draft Basin Plan Amendment 

 

2

 The Secretary of Resources has certified the planning process for Basin Plans as a regulatory program pursuant to 

PRC § 21080.5 and CEQA Guidelines §15251(g). This certification means basin planning is exempt from CEQA 

provisions that relate to preparing Environmental Impact Reports and Negative Declarations. The Basin Plan Staff 

Report satisfies the requirements of State Board Regulations for Implementation of CEQA, Exempt Regulatory 

Programs, which are found in the California Code of Regulations, Title 23, Division 3, Chapter 27, Article 6, 

beginning with Section 3775. 

Delta Methylmercury TMDL Report 6 April 2010 
staff report provides a detailed description of the CEQA scoping, Board, and public workshops 

and other stakeholder meetings that have taken place to date, including the formal Stakeholder 

Process. After staff has addressed any public comments on the draft TMDL and Basin Plan 

Amendment staff reports during the formal public review period, the final draft TMDL and Basin 

Plan Amendment staff reports will be presented to the Central Valley Water Board for their 

consideration in 2010. 

2.1.4 Units and Terms Used in this Report 

This report uses the term “total mercury” (TotHg) to indicate the sum of all forms of mercury 

(Hg) in water: physical states (e.g., dissolved, colloidal or particulate bound), chemical states 

(e.g., elemental, mercurous ion, or mercuric ion), organic compounds (e.g., 

monomethylmercury), and inorganic compounds (e.g., cinnabar). Monomethylmercury is the 

predominant form of organic mercury present in biological systems and will be noted in this 

report as “methylmercury” (MeHg). Because methylmercury typically composes only a small 

portion of total mercury in ambient water,3

 the phrases “inorganic mercury” and “total mercury” 

are sometimes used synonymously. 

Concentrations of methyl and total mercury in water (also referred to as “aqueous” methyl and 

total mercury) are reported in units of nanograms per liter (ng/l). Aqueous methylmercury 

concentrations are rounded to three decimal places and total mercury concentrations are 

rounded to two decimal places. Concentrations of suspended sediment are analyzed as total 

suspended solids (TSS) and use units of milligrams per liter (mg/l) rounded to one decimal 

place. In Chapter 7 (Source Assessment – Total Mercury & Suspended Sediment), the 

concentration of total mercury in suspended sediment is calculated as the ratio of 

concentrations of mercury to suspended sediments (TotHg:TSS). Units for the concentration of 

mercury in suspended sediment are part per million (ppm; equivalent to ng/mg or mg/kg), dry 

weight. Mercury levels in sediment and soil are also presented as part per million, dry weight. 

The units for loads of methylmercury and total mercury are grams per year (g/yr) and kilograms 

per year (kg/yr), respectively. Sediment loads are given in terms of millions of kilograms per 

year (kg/yr x 106

 or Mkg/yr). Water flow is presented in units of acre-feet per year or million 

acre-feet per year (M acre-ft) for annual rates, cubic feet per second (cfs) for instantaneous flow 

measurements, and million gallons per day (mgd) for treatment plants. Load calculations are 

typically rounded to two significant figures with calculations completed prior to rounding. For 

this draft report, additional significant figures occasionally were included to improve the reader’s 

ease in verifying calculations. 

Concentrations of mercury in fish tissue are reported as milligrams per kilogram (mg/kg), wet 

weight basis, rounded to two decimal places. Mercury is typically analyzed as “total mercury” in 

fish because of the additional cost required for methylmercury analysis. However, mercury 

exists almost entirely in the methylated form in small and top trophic level4

 fish (Becker and 

 

3

 For example, a comparison of average annual methylmercury and total mercury loads from tributary watersheds to 

the Delta (Tables 6.2 and 7.1) indicates that methylmercury loading comprises only about 2% of all total mercury 

loading from the tributaries. 4

 Trophic levels are numerical descriptions of an aquatic food web. The USEPA’s 1997 Mercury Study Report to 

Congress used the following criteria to designate trophic levels based on an organism’s feeding habits: 

Trophic level 1: Phytoplankton and bacteria. 

Trophic level 2: Zooplankton, benthic invertebrates and some small fish. 

Delta Methylmercury TMDL Report 7 April 2010 
Bigham, 1995; Nichols et al., 1999; Slotton et al., 2004). Therefore, even though all the fish 

mercury data presented in the report were generated by laboratory analyses for total mercury, 

the data are described as “methylmercury concentrations in fish”. 

Rates of fish consumption are given as grams of fish eaten per day (g/day) or meals per week. 

One adult human meal is assumed to be eight uncooked ounces (227 grams). Humans and 

wildlife species consume fish and other aquatic organisms from various size ranges and trophic 

levels. Safe fish tissue levels are identified in Chapter 4 for different trophic level and size 

classifications. These classifications are termed “trophic level food groups”. 

For this report, methylmercury fish tissue concentrations in trophic level food groups are 

recommended as the TMDL water quality targets. The tissue targets will be proposed as 

options for the Central Valley Water Board to consider when adopting fish tissue objectives. 

The term implementation goal in this report refers to methylmercury concentrations in 

standard 350-mm largemouth bass and unfiltered water, which are correlated to the targets. 

The implementation goal for methylmercury in unfiltered ambient water is Central Valley Water 

Board staff’s best estimate of the annual average methylmercury concentration in water needed 

to achieve the fish tissue targets. The “implementation goal” for methylmercury in ambient 

water is used to determine the methylmercury source load reductions necessary to meet the 

targets. The water and largemouth bass methylmercury goals are not being proposed as water 

quality objectives. 

2.2 Delta Characteristics and TMDL Scope 

2.2.1 Delta Geography 

The Sacramento-San Joaquin Delta, along with the San Francisco Bay, forms the largest 

estuary on the west coast of North America. The Delta encompasses a maze of over 

1,100 miles of river channels surrounding about 738,000 acres (1,153 square miles) of diked 

islands and tracts in Alameda, Contra Costa, Sacramento, San Joaquin, Solano and Yolo 

counties (Figure 1.1 and Figure A.1 in Appendix A). Many of the Delta waterways follow natural 

courses while others have been constructed to provide deep-water navigation channels, to 

improve water circulation, or to obtain material for levee construction (DWR, 1995). The legal 

boundary of the Delta is defined in California Water Code Section 12220. Appendix A illustrates 

the more than 100 named waterways addressed by this TMDL. 

The Delta and its source watersheds comprise nearly 40% of the landmass of the State of 

California (Table 2.1 and Figure 2.1). The Sacramento, San Joaquin, Mokelumne, Cosumnes, 

and Calaveras rivers all flow into the Delta, carrying approximately 47% of the State’s total 

runoff (DWR, 2005). Major reservoirs and lakes in the Sacramento Basin include Shasta, 

Whiskeytown, Oroville, Englebright, Camp Far West, Folsom, Black Butte, Indian Valley, Clear 

Lake and Lake Berryessa. Major reservoirs and lakes in the San Joaquin Basin include 

Camanche, New Hogan, New Melones/Tulloch, Don Pedro, McClure, Burns, Bear, Owens, 

Eastman, Hensley, Millerton and Marsh Creek. 

 

Trophic level 3: Organisms that consume zooplankton, benthic invertebrates, and other TL2 organisms. 

Trophic level 4: Organisms that consume TL3 organisms. 

Delta Methylmercury TMDL Report 8 April 2010 
The legal Delta encompasses the southern two thirds of the Yolo Bypass, a 73,300-acre 

floodplain on the west side of the lower Sacramento River. The Fremont and Sacramento Weirs 

route floodwaters from the Sacramento River and its associated tributary watersheds around the 

Sacramento urban area to the Yolo Bypass. Cache and Putah Creeks, Willow Slough, and the 

Knights Landing Ridge Cut from the Colusa Basin all drain directly to the Yolo Bypass. 

The Sacramento River contributes an average annual water volume of 18.3 million acre-feet 

and the Yolo Bypass and the San Joaquin River contribute an average of 5.8 million acre-feet. 

Diversions in the Delta include the State Water Project (Banks Pumping Plant and the North 

Bay Aqueduct), Central Valley Project (Tracy Pumping Plant), and Contra Costa Water District, 

which withdraw average annual water volumes of about 3.7 million, 2.5 million, and 

126 thousand acre-feet, respectively (DWR, 2005). During a typical water year,5

 the Delta 

receives runoff only from the Sacramento and San Joaquin Basins in the Central Valley 

(Figure 2.1). During infrequent flood events, the Tulare Basin in the southern Central Valley 

connects with the San Joaquin River system. 

The mean annual precipitation in the City of Stockton in the eastern Delta is approximately 

14 inches, with the majority of rain falling between November and March. Temperatures at 

Stockton typically average 62 degrees Fahrenheit (o

F), with summer highs exceeding 90 oF and 

winter lows dropping below 40 oF. 

The Delta had a population of 410,000 people in 1990 (DWR, 1995). As of the 2000 Census, 

about 462,000 people resided in the Delta region (DWR, 2005). Rapid growth is occurring in 

urban areas in and surrounding the Delta, especially in Elk Grove (27% growth per year – the 

highest growth rate in California), Tracy (5.9% per year), Brentwood (12.3% per year), and Rio 

Vista (11.1% per year). 

Agriculture and recreation are the two primary businesses in the Delta. The Delta also provides 

habitat for over five hundred species of wildlife (DWR, 1995; Herbold et al., 1992). The Delta is 

the major source of fresh water to San Francisco Bay and supplies drinking water for over twothirds of the State’s population (over 23 million people) and irrigation water for more than seven 

million acres of farmland statewide (DWR, 2005). Table 2.2 lists additional features of the 

Delta. 

 

5

 A “water year” (WY) is defined as the period between 1 October and 30 September of the following year; for 

example, WY2001 is the period between 1 October 2000 and 30 September 2001. Water year types in California 

are classified according to the natural water production of the major basins. See Appendix E for more information 

about water year classifications. 

Delta Methylmercury TMDL Report 9 April 2010 
Figure 2.1: The Central Valley

Delta Methylmercury TMDL Report 10 April 2010 
Table 2.1: Spatial Perspective of the Delta and Its Source Regions

Region Acres Square Miles 

% of 

California 

% of 

Central Valley 

California 101,445,246 158,508 --- --- 

Central Valley 37,982,554 59,348 37% --- 

Delta (legal boundary) 737,630 1,153 1% 1.9% 

Delta Watershed (Statutory Delta & all 

tributary watersheds that ultimately drain 

directly to the Delta) 

27,226,796 42,542 27% 72% 

Delta Watershed Area 

Downstream of Major Dams 12,469,054 19,483 12% 33% 

Sacramento River Watershed 17,410,314 27,204 17% 46% 

San Joaquin River Watershed 9,801,103 15,314 10% 26% 

Table 2.2: Key Delta Features (DWR, 1995 and 2005) 

Population: 410,000 (1990), 462,000 (2000) 

Incorporated cities 

entirely within the Delta: 

Antioch, Brentwood, Isleton, 

Pittsburg, Tracy 

Major cities partly within 

the Delta: 

Sacramento, Stockton, 

West Sacramento 

Area (acres): Agriculture: 538,000 

Cities & towns: 64,000 

Water surface: 61,000 

Undeveloped: 75,000 

Total: 738,000 

# of unincorporated towns 

and villages: 

14 Total length of all 

leveed channels: 

1,100 miles (1987) 

Diversions from the 

Delta:

Central Valley Project 

State Water Project 

Contra Costa Canal 

City of Vallejo 

Western Delta Industry 

1,800+ Agricultural diversions 

Main crops: Alfalfa 

asparagus 

corn 

fruit 

grain & hay 

grapes 

pasture 

safflower 

sugar beets 

tomatoes 

Rivers flowing into 

the Delta:

Calaveras San Joaquin 

Cosumnes Mokelumne 

Sacramento 

Fish and wildlife: # of Federal & # of Non-Native 

 # of Species (a) State Species of Concern (a) Species (b)

Birds: 230 7 3 

Mammals: 45 9 7 

Fish: 52 8 30 

Reptiles & amphibians: 25 6 1 

Flowering plants: 150 54 70 

Invertebrates: na 21 13 

Major anadromous fish: American shad, salmon, steelhead trout, striped bass, sturgeon 

(a) Endangered, threatened, and candidate species per the federal and State listings as cited in the Sacramento – San Joaquin 

Delta Atlas (DWR, 1995) and updated using the California Department of Fish and Game’s Natural Diversity Database, 

accessed January 2010 (CDFG, 2010). 

(b) Introduced species in the Sacramento – San Joaquin Delta, as cited in the Sacramento – San Joaquin Delta Atlas (DWR, 

1995). 

Delta Methylmercury TMDL Report 11 April 2010 
2.2.2 TMDL Scope & Delta Subareas 

This TMDL addresses fish mercury impairment in all waterways within the legal Delta, except 

the westernmost portion of the Delta near Chipps Island that falls within the jurisdiction of the 

San Francisco Bay Regional Water Quality Control Board (Figure 2.2; see Appendix A for a list 

of named waterways). Tributaries are considered to be nonpoint sources to the Delta and are 

evaluated at or near the locations where they cross the statutory Delta boundary. Assessment 

of point and nonpoint sources that contribute to tributary discharges to the Delta is ongoing and 

will be described in reports for future mercury TMDL programs for those watersheds and 

implementation activities for the Delta methylmercury TMDL. 

The methylmercury source analysis and linkage analysis for the Delta TMDL divide the Delta 

into eight regions based on the hydrologic characteristics and mixing of the source waters 

(Figure 2.2) (e.g., DWR, 1991 and 1962). A hydrology-based methylmercury TMDL is proposed 

in this report as it more accurately reflects the concentrations and sources of methylmercury 

and the extent of fish impairment. As described in Chapter 8 (Allocations), essentially a 

separate methylmercury allocation scheme is developed for each subarea because the 

methylmercury sources and level of fish impairment in each subarea are different. The following 

paragraphs describe the delineation of the hydrologic subareas. These subareas are different 

from the Delta water body segment delineation (“portions”) defined by the State Water Board for 

the 2006 Clean Water Act Section 303(d) List (SWRCB-DWQ, 2006). 

Sacramento River: This subarea is dominated by Sacramento River flows. It is bound to the 

east by the legal Delta boundary and to the west by the eastern levee of the Sacramento Deep 

Water Ship Channel. Sacramento River flows influence the Upper and Lower Mokelumne River 

in the Delta because of diversions by the Delta Cross Channel near Walnut Grove (Figure A.1 in 

Appendix A). The Delta Cross Channel controls diversions of fresh water from the Sacramento 

River to Snodgrass Slough and the Mokelumne River to combat salt-water intrusion in the Delta, 

to dilute local pollution, and to more efficiently supply the federal Central Valley Project and 

State Water Project pumps in the southern Delta. Although drawn as a line, the Sacramento 

River subarea’s boundary with the South Yolo Bypass, Central Delta, and West Delta subareas 

is defined by a gradient in water quality characteristics that varies with the tidal cycle, magnitude 

of wet weather flows, diversions by within-Delta control structures, and releases from reservoirs 

in the upstream watersheds. 

Yolo Bypass - North & South: The Yolo Bypass is a 73,300-acre floodplain on the west side of 

the lower Sacramento River (see Section E.2.2 and Figure E.2 in Appendix E for the floodplain 

boundary definition). The Fremont and Sacramento Weirs route floodwaters to the Yolo Bypass 

from the Sacramento and Feather Rivers and their associated tributary watersheds. Cache and 

Putah Creeks, Willow Slough, and the Knights Landing Ridge Cut from the Colusa Basin all 

drain directly to the Yolo Bypass. The legal Delta encompasses only the southern two thirds of 

the Yolo Bypass. The “Yolo Bypass – North” subarea is defined by Fremont Weir to the north 

and Lisbon Weir to the south and includes areas within and north of the legal Delta boundary. 

The “Yolo Bypass – South” subarea is defined by Lisbon Weir to the north and the southern end 

of Cache Slough to the south. Lisbon Weir (Figure E.2) limits the range of tidal fluctuation 

upstream in the Yolo Bypass. 

Delta Methylmercury TMDL Report 12 April 2010 
Figure 2.2: Hydrology-Based Delineation of Subareas within the Legal Delta and Yolo Bypass 

Delta Methylmercury TMDL Report 13 April 2010 
Cosumnes/Mokelumne Rivers: This subarea includes the lower Cosumnes and Mokelumne 

Rivers and is defined by the legal Delta boundary to the east and the Delta Cross Channel 

confluence with the Mokelumne to the west. 

San Joaquin River: This subarea is defined by the legal Delta boundary to the east and south, 

and Grantline Canal and the beginning of the Stockton Deep Water Channel to the north. At 

present, the San Joaquin River is almost entirely diverted out of the Delta by way of Old River 

and Grantline Canal for export south of the Delta via the state and federal pumping facilities 

near Tracy. 

Marsh Creek: This subarea is defined by the portion of the Marsh Creek watershed within the 

legal Delta boundary that is upstream of tidal effects. 

West Delta: The West Delta subarea encompasses the confluence of the Sacramento and San 

Joaquin Rivers, which transport water from the Central Valley to the San Francisco Bay. The 

western border of the West Delta subarea is defined by the jurisdictional boundary between the 

Central Valley Regional Water Quality Control Board (Region 5) and the San Francisco Water 

Board (Region 2) (Figure 2.2). Water quality characteristics are determined by the tidal cycle, 

magnitude of wet weather flows, controlled flow diversions by within-Delta structures, and 

releases from reservoirs in the upstream watersheds. 

Central Delta: The Central Delta includes a myriad of natural and constructed channels that 

transport water from the upper watersheds to San Francisco Bay to the west and the state and 

federal pumps to the southwest. The Central Delta tends to be most influenced by waters from 

the Sacramento River. 

2.3 Mercury Effects & Sources 

2.3.1 Mercury Chemistry and Accumulation in Biota 

Mercury (Hg) can exist in various forms in the environment. Physically, mercury can exist in 

water in a dissolved, colloidal or particulate bound state. Chemically, mercury can exist in three 

oxidation states: elemental (Hgo

), mercurous ion (monovalent, Hg+), or mercuric ion (divalent, 

Hg+2). Ionic mercury can react with other chemicals to form both organic and inorganic 

compounds, such as cinnabar (HgS), and can be converted by sulfate reducing bacteria to more 

toxic organic compounds, such as monomethylmercury (CH3Hg) or dimethylmercury ((CH3)2Hg). 

Important factors controlling the conversion rate of inorganic to organic mercury include 

temperature, percent organic matter, redox potential, salinity, pH, and mercury concentration. 

Monomethylmercury is the predominant form of organic mercury present in biological systems 

and will be noted in this report as methylmercury or “MeHg”. Because dimethylmercury is an 

unstable compound that dissociates to monomethylmercury at neutral or acid pH, it is not a 

concern in freshwater systems (USEPA, 1997a). Chapter 3 provides more information about 

potentially controllable methylation processes in the Delta region. 

Both inorganic and organic mercury can be taken up by aquatic organisms from water, 

sediments and food. Low trophic level species such as phytoplankton obtain all their mercury 

directly from the water. Bioconcentration describes the net accumulation of mercury directly 

Delta Methylmercury TMDL Report 14 April 2010 
from water. The bioconcentration factor is the ratio of mercury concentration in an organism to 

mercury concentration in water. Mercury may also accumulate in aquatic organisms from 

consumption of mercury-contaminated prey (USEPA, 1997b). Mercury bioaccumulates in 

organisms when rates of uptake are greater than rates of elimination. 

Repeated consumption and accumulation of mercury from contaminated food sources results in 

tissue concentrations of mercury that are higher in each successive level of the food chain. 

This process is termed biomagnification. Methylmercury accumulates within organisms more 

than inorganic mercury because inorganic mercury is less well absorbed and/or more readily 

eliminated than methylmercury. The proportion of mercury that exists as the methylated form 

generally increases with the level of the food chain. Methylmercury comprises 85% to 100% of 

the total mercury measured in fish (Becker and Bigham, 1995; Nichols et al., 1999; 

Slotton et al., 2004). 

Consumption of contaminated, high trophic level fish is the primary route of methylmercury 

exposure. For example, the aquatic food web provides more than 95% of humans’ intake of 

methylmercury (USEPA, 1997a). Wildlife species of potential concern that consume fish and 

other aquatic organisms from the Delta include piscivorous fish, herons, egrets, mergansers, 

grebes, bald eagle, kingfisher, peregrine falcon, osprey, mink, raccoon and river otter. 

2.3.2 Toxicity of Mercury 

Mercury is a potent neurotoxicant. Methylmercury is the most toxic form of this metal. 

Methylmercury exposure causes multiple effects, including tingling or loss of tactile sensation, 

loss of muscle control, blindness, paralysis, birth defects and death. Adverse neurological 

effects in children appear at dose levels five to ten times lower than associated with toxicity in 

adults (NRC, 2000). Children may be exposed to methylmercury during fetal development, by 

eating fish, or through both modes. Effects of methylmercury are dose dependent. 

Wildlife species may also experience neurological, reproductive or other detrimental effects from 

mercury exposure. Behavioral effects such as impaired learning, reduced social behavior and 

impaired physical abilities have been observed in mice, otter, mink and macaques exposed to 

methylmercury (Wolfe et al., 1998). Reproductive impairment following mercury exposure has 

been observed in multiple species, including common loons and western grebe (Wolfe et al., 

1998), walleye (Whitney, 1991 in Huber, 1997), mink (Dansereau et al., 1999) and fish (Huber, 

1997; Wiener and Spry, 1996). 

2.3.3 Mercury Sources & Historic Mining Activities 

Identified sources of methyl and total mercury in the Delta and in tributary watersheds include 

geothermal springs, methylmercury flux from sediments in wetlands and open water habitats, 

municipal and industrial dischargers, agricultural drainage, urban runoff, atmospheric 

deposition, and erosion of naturally mercury-enriched soils and excavated overburden and 

tailings from historic mining operations. Although none are present within the legal Delta, 

historic mercury and gold mining sites – along with their associated contaminated waterways – 

may contribute a substantial portion of the total mercury in the tributary discharges to the Delta. 

Delta Methylmercury TMDL Report 15 April 2010 
Chapters 6 and 7 provide a detailed assessment of the within-Delta sources of methyl and total 

mercury. 

As noted in source analyses in Chapters 6 and 7, tributary inputs to the Delta are the largest 

sources of methyl and total mercury. These tributaries drain many of the major mercury mining 

districts in the Coast Range and the placer gold mining fields in the Sierra Nevada Mountains. 

The Coast Range is a region naturally enriched in mercury. Active geothermal vents and hot 

springs deposit mercury, sulfur, and other minerals at or near the earth’s surface. Most of the 

mercury deposits in California occur within a portion of the Coast Range geomorphic province 

extending from Clear Lake in Lake County in the north to Santa Barbara County in the south. 

Approximately 90% of the mercury (roughly 104 million kilograms) used in the United States 

between 1846 and 1980 was mined in the Coast Range of California (Churchill, 2000). Much of 

the mining and extraction occurred prior to 1890 when mercury processing was crude and 

inefficient. The ore was processed at the mine sites, with about 35 million kilograms of mercury 

lost at the mine sites. As a result, high levels of mercury are present in sediment and fish tissue 

in Coast Range water bodies. Fish advisories have been posted for Clear Lake, Cache Creek, 

Lake Berryessa and Black Butte Reservoir (Stratton et al., 1987; Brodberg and Klasing, 2003; 

Gassel et al., 2005). Mercury mine waste enters the Delta from mine-impacted Coast Range 

creeks such as Cache, Putah and Marsh Creeks. 

Approximately 10 million kilograms of Coast Range mercury were transported across the valley 

and used as an amalgam in placer and lode gold mining in the Sierra Nevada Mountains 

between 1850 and 1890 (Churchill, 2000). Approximately six million kilograms of mercury were 

lost in Sierra Nevada rivers and streams during gold mining operations. Principal gold mining 

areas were in the Yuba River and Bear River (tributaries to the Sacramento River via the 

Feather River), the Cosumnes River (a tributary to the Mokelumne River), and the Stanislaus, 

Tuolumne and Merced Rivers (tributaries to the San Joaquin River). Elevated mercury 

concentrations are present in fish in all these Sierra Nevada waterways. Floured6

 elemental 

mercury enters the Delta from the Sacramento, Mokelumne and San Joaquin Rivers. 

Evaluation of legacy mine sites, associated contaminated waterway reaches, and other methyl 

and total mercury sources that contribute to tributary inputs to the Delta is ongoing. More 

detailed source analyses for the tributary watersheds will be conducted by future mercury TMDL 

programs for those watersheds and by proposed implementation actions for the Delta mercury 

control program (see Chapter 4 in the draft Basin Plan Amendment staff report). 

 

6

 Flouring is the division of mercury into extremely small globules, which gives it a white, flour-like appearance. If the 

floured mercury has surface impurities such as oil, grease, clay or iron and base metal sulfides, it will not coalesce 

into larger drops or form an amalgam with gold (Beard, 1987). Mercury was used for gold recovery throughout the 

Sierra Nevada. Floured mercury was formed by the pounding of boulders and gravels over liquid mercury in 

hydraulic mining-related sluice boxes (Hunerlach et al., 1999), as well by intense grinding in the hardrock milling 

systems, and was transported downstream with tailings. 

Delta Methylmercury TMDL Report 16 April 2010 
2.4 Beneficial Uses, Applicable Standards & Extent of Impairment 

2.4.1 Sacramento-San Joaquin Delta Estuary Beneficial Uses 

The federal Clean Water Act and the State Water Code (Porter-Cologne Water Quality Control 

Act) require the State to identify and protect the beneficial uses of its waters. Table 2.3 lists the 

existing beneficial uses of the Delta. Human consumption of fish and shellfish (currently 

assumed under REC-1) and wildlife habitat (WILD) are impaired because of elevated mercury 

concentrations in fish throughout the Delta. The Basin Plan does not include a commercial and 

sport fishing (COMM) designation for the Delta, which includes uses of water for commercial or 

recreational collection of fish, shellfish, or other organisms intended for human consumption or 

bait purposes. However, as described in Appendix C, commercial and sport fishing take place 

in the Delta. Some sport and commercial species (e.g., striped bass and largemouth bass) are 

impaired by mercury, while others (e.g., salmon and clams) are not. The draft Basin Plan 

Amendment staff report considers adoption of a COMM beneficial use for the Delta. 

The municipal and industrial supply (MUN) beneficial use is designated in the Basin Plan for all 

waterways within the legal Delta boundary except Marsh Creek and Yolo Bypass (e.g., Cache 

Creek Settling Basin outflow, Prospect Slough, and the downstream segment of Putah Creek 

within the Yolo Bypass). Staff evaluated whether levels of total mercury in water in Delta 

waterways support the MUN beneficial use. The California Toxics Rule (CTR) criterion for 

mercury protects humans from exposure to mercury through fish consumption and drinking 

water and is enforceable for all waters with a municipal and domestic water supply or aquatic 

beneficial use designation. As described in Sections 2.4.2 and 7.4.2, the CTR mercury criterion 

is exceeded in outflow from the Cache Creek Settling Basin and possibly in Prospect Slough, 

Putah Creek, and Marsh Creek; however, MUN is not designated for these waterways. Mercury 

reductions may be needed to meet the CTR in the Yolo Bypass downstream of the Cache 

Creek Settling Basin and in Marsh Creek, but these reductions will be addressed by the existing 

TMDL for Cache Creek and future TMDLs for the Marsh Creek and Putah Creek watersheds 

(see Section 7.4.2), in addition to actions designed to reduce fish methylmercury concentrations 

in the Delta/Yolo Bypass and total mercury exports to San Francisco Bay (see Section 8.2). 

Space intentionally left blank. 

Delta Methylmercury TMDL Report 17 April 2010 
Table 2.3: Beneficial Uses of the Delta and Yolo Bypass (a)

Beneficial Use 

Delta 

Status 

Yolo Bypass 

Status 

Municipal and domestic supply (MUN) Existing (b)

Agriculture – irrigation and stock watering (AGR) Existing Existing 

Industry – process (PROC) and service supply (IND) Existing 

Contact recreation (REC-1) (c) Existing (b) Existing (b)

Non-contact recreation (REC-2) (c) Existing Existing 

Freshwater habitat (warm water species) Existing Existing 

Freshwater habitat (cold water species) Existing Potential 

Spawning, reproduction and/or early development of fish (SPWN) 

(warm water species) Existing Existing 

Wildlife habitat (WILD) Existing (b) Existing (b)

Migration of aquatic organisms (MIGR) (warm and cold water 

species) Existing Existing 

Navigation (NAV) Existing 

(a) This table lists the beneficial uses designated for the Delta and Yolo Bypass in Table II-1 of the 

Water Quality Control Plan for the Sacramento River and San Joaquin River Basins (Basin Plan) 

(CVRWQCB, 2009). The Yolo Bypass is a 73,300-acre floodplain on the west side of the lower 

Sacramento River. The lower two thirds of the Yolo Bypass are within the legal Delta, and 

waterways within the entire Delta are included in Clean Water Act 303(d) List. However, Table II 1 of 

the Basin Plan includes separate table rows for the Yolo Bypass and Delta. 

(b) These are beneficial uses impaired by mercury in the Delta, including portions of the Yolo Bypass 

within the legal Delta boundary. 

(c) REC-1 includes recreational activities involving body contact with water, where ingestion of water is 

reasonably possible. These uses include, but are not limited to, swimming, wading, water-skiing and 

fishing. REC-2 includes recreational activities involving proximity to water, but where there is 

generally no body contact with water, nor any likelihood of ingestion of water. These uses include, 

but are not limited to, picnicking, sunbathing, hiking, beachcombing, camping, boating, hunting and 

sightseeing. 

2.4.2 Applicable Standards & Extent of Impairment 

The narrative water quality objective for toxicity in the Basin Plan states, “All waters shall be 

maintained free of toxic substances in concentrations that produce detrimental physiological 

responses in human, plant, animal, or aquatic life.” The narrative toxicity objective further says 

that “The Regional Water Board will also consider ... numerical criteria and guidelines for toxic 

substances developed by the State Water Board, the California Office of Environmental Health 

Hazard Assessment, the California Department of Health Services, the U.S. Food and Drug 

Administration, the National Academy of Sciences, the USEPA, and other appropriate 

organizations to evaluate compliance with this objective” (CVRWQCB, 2009). Four potential 

criteria were evaluated to determine whether the Delta was in compliance with the narrative 

objective. They are the USEPA and USFWS fish tissue criteria for protection of humans and 

wildlife, the USEPA aqueous methylmercury criterion for drinking water, the United Nations 

aqueous total mercury guidance level to protect livestock, and the California Toxic Rule (CTR) 

aqueous total mercury criterion for protection of human and wildlife health. Each is reviewed 

below and a determination made as to whether the recommended criteria or objective is met in 

the Delta. 

Delta Methylmercury TMDL Report 18 April 2010 
2.4.2.1 Fish Tissue Criteria 

In 1971, a human health advisory was issued for the Sacramento-San Joaquin Delta advising 

pregnant women and children not to consume striped bass. In 1994, an interim advisory was 

issued by the California Office of Environmental Health Hazard Assessment (OEHHA) for San 

Francisco Bay and Delta recommending no consumption of large striped bass and shark 

because of elevated concentrations of mercury and polychlorinated biphenyls (OEHHA, 1994). 

Additional monitoring indicates that several more species, including largemouth bass and white 

catfish (two commonly-caught local sport fish), also have elevated concentrations of mercury in 

their tissue (Davis et al., 2003; Slotton et al., 2003; LWA, 2003; SWRCB-DWQ, 2002). 

In 2009, OEHHA issued updated safe eating guidelines for the Central and South Delta 

(including San Joaquin River from the Port of Stockton to Pittsburg), the San Joaquin River from 

Friant Dam to the Port of Stockton, the Sacramento River and Northern Delta, the lower 

Cosumnes River, and the lower Mokelumne River7

 (OEHHA, 2009). OEHHA advises that 

pregnant and nursing women and children avoid consuming bass (largemouth and striped) and 

Sacramento pikeminnow from the San Joaquin, Sacramento and lower Cosumnes and lower 

Mokelumne Rivers. In the Central and South Delta waterways, pregnant and nursing women 

and children should limit consumption of largemouth bass, carp, and crappie to 8 ounces 

uncooked fish (1 serving) per week and bluegill, catfish, and crayfish to 16 ounces uncooked 

(2 servings) per week. The new guidelines identify fish species that can safely be eaten in 2 or 

more servings per week. 

The Delta was listed for mercury because of the 1971 and 1994 fish advisories and because 

some fish tissue concentrations exceeded the National Academy of Sciences (NAS) guidelines 

for protection of wildlife health. The NAS wildlife guideline is 0.5 mg/kg mercury in whole, 

freshwater fish (NAS, 1973). The USEPA has since published a recommended criterion for the 

protection of human health of 0.3 mg/kg mercury in fish tissue (USEPA, 2001). Similarly, the 

USFWS has provided guidance on safe methylmercury ingestion rates for sensitive wildlife 

species (USFWS, 2002, 2003 and 2004). The Delta TMDL cites the USEPA and USFWS 

recommended criteria for protection of human and wildlife health, as these are more protective. 

Significant regional variations in fish tissue mercury concentrations are observed in the Delta. 

Elevated concentrations occur along the periphery of the Delta while lower body burdens are 

measured in the central Delta. A summary of fish tissue methylmercury concentrations by Delta 

subarea is provided in Chapter 4 (Tables 4.7 and 4.10) and Appendix C. Concentrations are 

greater than recommended as safe by the USEPA and USFWS at all locations except in the 

central Delta. Percent reductions in fish methylmercury levels ranging from 0% to 80% in the 

peripheral Delta subareas will be needed to meet the numeric targets for wildlife and human 

health protection. 

 

7

 OEHHA’s recent advisories are in the form of safe eating guidelines that indicate which fish species may be eaten 

safely as well as those that should be avoided or eaten less frequently. 

Delta Methylmercury TMDL Report 19 April 2010 
2.4.2.2 Aqueous Criteria & Guidance 

The USEPA recommends a safe level of 70 ng/l methylmercury in drinking water to protect 

humans (USEPA, 1987). This level was released through USEPA's Integrated Risk Information 

System (IRIS) and was based on USEPA's recommended methylmercury reference dose for 

lifetime exposure. Methylmercury concentrations in the Delta typically range from 0.02 to 

0.3 ng/l (Section 6.2.1). The maximum observed concentration in the Delta between March 

2000 and April 2004 was 0.70 ng/l in Prospect Slough in March 2000 (Appendix L). The 

USEPA IRIS drinking water criterion is not expected to be exceeded in the Delta. 

The United Nations recommends a guidance level of 10,000 ng/l unfiltered total mercury to 

protect livestock drinking water (Ayers and Westcot, 1985). Unfiltered mercury concentrations 

in the Delta typically range from 0.26 to 100 ng/l (Table 7.4 in Chapter 7). The maximum 

concentration ever observed in the Delta was 696 ng/l at Prospect Slough on January 10, 1995. 

The United Nations recommended livestock guidance level is not expected to be exceeded in 

the Delta. 

The USEPA promulgated the CTR in April 2000 (USEPA, 2000b). The CTR mercury criterion is 

0.05 μg/L (50 ng/l) total recoverable mercury for freshwater sources of drinking water. The CTR 

criterion was developed to protect humans from exposure to mercury in drinking water and in 

contaminated fish. It is enforceable for all waters with beneficial use designations of municipal 

and domestic water supply. This includes all subareas of the Delta except Yolo Bypass and 

Marsh Creek. As indicated earlier in Table 2.3, Basin Plan Table II-1 does not designate “MUN” 

for the Yolo Bypass and Marsh Creek; however, it does designate recreation (including fish 

consumption by humans). The CTR does not specify duration or frequency. The Central Valley 

Water Board has previously employed a 30-day-averaging period with an allowable exceedance 

frequency of once every three years.8

 

An evaluation of unfiltered total mercury concentrations demonstrates that the CTR mercury 

criterion is not exceeded anywhere in the Delta. Mercury concentrations are greater than the 

CTR criterion downstream of the Cache Creek Settling Basin in the Yolo Bypass and possibly in 

Putah Creek outflow to Yolo Bypass, Prospect Slough and Marsh Creek (Section 7.4.2). These 

water bodies are not designated for MUN. The mercury concentrations greater than the CTR 

criterion downstream of Cache Creek may be addressed by the Cache Creek mercury control 

program (Cooke and Morris, 2005) adopted in October 2005 and proposed upgrades of the 

Cache Creek Settling Basin described in Chapter 4 of the draft Basin Plan Amendment staff 

report. Prospect Slough is downstream of Cache Creek and potential exceedances of the CTR 

could be corrected with decreases in mercury loads from Cache Creek and its settling basin. 

Putah and Marsh Creeks are both on the 303(d) list because of elevated mercury 

concentrations. Potential exceedance of the CTR downstream of these water bodies will be 

addressed by load reductions to be determined by their TMDLs. Chapters 7 and 8 will provide 

additional evaluations of total mercury loads from these watersheds and potential reduction 

strategies. 

Regardless of whether MUN is specifically designated by the Basin Plan (and the CTR criterion 

is enforceable), the numeric targets and mercury control actions in this and other TMDLs will 

 

8

 Personal communication from P. Woods (USEPA Region 9) to J. Marshack (CVRWQCB), 4 December 2001. 

Delta Methylmercury TMDL Report 20 April 2010 
ensure that the CTR’s level of human health protection is met throughout the Delta and Yolo 

Bypass. The CTR mercury criterion protects human health and is intended to be used where 

consumption of aquatic organisms occurs, which includes the Delta with the Marsh Creek 

subarea and Yolo Bypass. The proposed fish tissue objective will also apply to all of the Delta 

subareas and the Yolo Bypass. Since the proposed fish tissue objectives are more stringent 

than the CTR mercury criterion, attainment of the fish tissue objectives will also meet the aim of 

the CTR for protection of people that eat local fish. 

The USFWS and the U.S. National Marine Fisheries Service are concerned that the mercury 

objective in the CTR may not protect threatened and endangered species and requested that 

the USEPA reevaluate the criterion. The USEPA has not released a reevaluation. Staff 

developed the TMDL’s wildlife target evaluation and the Basin Plan amendments’ proposed fish 

tissue objective for small fish with guidance from USFWS to ensure that threatened and 

endangered species will be protected. 

2.4.2.3 San Francisco Bay Mercury TMDL’s Allocation for Total Mercury 

in Central Valley Outflows 

As a component of the mercury control program for the San Francisco Bay, San Francisco 

Water Board staff developed a target for San Francisco Bay sediment mercury concentration 

(particle-bound mercury mass divided by sediment mass) of 0.2 mg/kg and assigned the Central 

Valley a five-year average total mercury load allocation of 330 kg/yr at Mallard Island or a 

decrease of 110 kg/yr in mercury sources to the Delta (Johnson and Looker, 2004; 

SFBRWQCB, 2006). Compliance with the allocation can be assessed by one of two methods: 

“First, attainment may be demonstrated by documentation provided by the 

Central Valley Water Board that shows a net 110 kg/yr decrease in total mercury 

entering the Delta from within the Central Valley region. Alternatively, attainment 

of the load allocation may be demonstrated by multiplying the flow-weighted 

suspended sediment mercury concentration by the sediment load measured at 

the RMP Mallard Island monitoring station. If sediment load estimates are 

unavailable, the load shall be assumed to be 1,600 million kg of sediment per 

year. The mercury load fluxing past Mallard Island will be less than or equal to 

330 kg/yr after attainment of the allocation.” 

(San Francisco Bay Basin Plan, Chapter 7) 

Central Valley Water Board staff will recommend to the Central Valley Water Board that the 

110 kg total mercury reduction be met by reductions in total mercury entering the Delta from 

within the Central Valley. Initial reduction efforts should focus on the Cache Creek, Feather 

River, American River, Cosumnes River and Putah Creek watersheds because they export the 

largest volume of highly contaminated sediment (see Chapter 8 in this TMDL report and 

Chapter 4 in the draft Basin Plan Amendment staff report). Load calculation methods and 

strategies for reducing total mercury loading to San Francisco Bay are discussed more in 

Chapters 7 and 8 of this report and in the draft Basin Plan Amendment staff report. 

Delta Methylmercury TMDL Report 21 April 2010 
Key Points 

• The federal Clean Water Act (CWA) requires States to identify water bodies that do not meet 

their designated beneficial uses and to develop programs to eliminate impairments. States 

refer to the control program as a Total Maximum Daily Load (TMDL) program. A TMDL is the 

total maximum daily load of a pollutant that a water body can assimilate and still attain 

beneficial uses. 

• The State of California Porter-Cologne Water Quality Control Act requires the Central Valley 

Water Board to develop a water quality control plan for each water body in the Central Valley 

that does not meet its designated beneficial uses. The Water Quality Control Plan for the 

Sacramento River and San Joaquin River Basins (the Basin Plan) is the legal document that 

describes the beneficial uses of all water bodies in these basins, adopted water quality 

objectives to protect them, and, if the objectives are not being met, an implementation 

program to correct the impairment. 

• This draft TMDL report addresses scientific peer review comments on the June 2006 draft 

TMDL report, Central Valley Water Board member comments and questions voiced during the 

March 2007 workshop, additional input from agencies and stakeholders during the 2008-2009 

Stakeholder Process, and supplementary evaluations to support the Basin Planning effort 

described in the draft Basin Plan Amendment staff report. After staff has addressed any 

public comments on this draft TMDL and Basin Plan Amendment staff reports, the final draft 

Basin Plan Amendment staff report will be presented to the Central Valley Water Board for 

their consideration later in 2010. 

• In 1990 the Central Valley Water Board identified the Delta as impaired by mercury because 

fish had elevated levels of mercury that posed a risk for human and wildlife consumers. In 

addition, the San Francisco Bay mercury control program identified Central Valley outflows via 

the Delta as one of the principal sources of total mercury to San Francisco Bay and assigned 

the Central Valley a load reduction of 110 kg/yr. Therefore, the final mercury TMDL control 

plan for the Delta must ensure protection of human and wildlife health in the Delta and meet 

the San Francisco Bay load allocation for the Central Valley. 

• The scope of the Delta methylmercury TMDL includes all waterways within the legal Delta 

boundary and the Yolo Bypass north of the Delta. This TMDL addresses both methyl and total 

mercury. Reductions in methylmercury concentrations in ambient water are required to reduce 

methylmercury concentrations in fish. Reductions in total mercury loads are needed to 

maintain compliance with the USEPA’s criterion of 50 ng/l; to prevent increases in total 

mercury discharges from causing increases in water and fish methylmercury in the Delta, 

thereby worsening the impairment; to meet the San Francisco Bay TMDL allocation to the 

Central Valley; and to reduce methylmercury production in Delta waterways. 

• Elevated fish mercury concentrations occur along the periphery of the Delta while lower body 

burdens are measured in the central Delta. Concentrations are greater than recommended as 

safe by the USEPA and USFWS at all locations except in the central Delta. Percent 

reductions in fish methylmercury levels ranging from 0% to 80% in the peripheral Delta 

subareas will be needed to meet the numeric targets for wildlife and human health protection. 

Delta Methylmercury TMDL Report 22 April 2010 
3 POTENTIALLY CONTROLLABLE METHYLATION PROCESSES IN THE DELTA 

The primary problem with mercury in the Delta’s aquatic ecosystems can be defined as biotic 

exposure to methylmercury (Wiener et al., 2003a). Therefore, decreasing biotic exposure to 

methylmercury is the ultimate goal of the Delta methylmercury TMDL and implementation 

program. Several published papers provide comprehensive reviews of the current knowledge of 

the methylmercury cycle (e.g., Wiener et al., 2003a and 2003b; Tetra Tech, Inc., 2005a; LWA, 

2002). This chapter focuses on the processes that are potentially controllable in the Delta. The 

concepts summarized in this chapter guided the development of the methylmercury TMDL for 

the Delta, particularly the linkage analyses (Chapter 5), methyl and total mercury source 

analyses (Chapters 6 and 7), and recommended methylmercury allocations and total mercury 

limits (Chapter 8). Data gaps and uncertainties associated with each factor are identified in this 

chapter and then addressed further by recommendations for source characterization and control 

studies in Chapter 4 of the draft Basin Plan Amendment staff report. 

Methylmercury concentrations in aquatic ecosystems are the result of two competing processes: 

methylation and demethylation. Methylation is the addition of a methyl group (CH3) to an 

inorganic mercury molecule (Hg+2). Sulfate reducing bacteria are the primary agents 

responsible for the methylation of mercury in aquatic ecosystems (Compeau and Bartha, 1985; 

Gilmour et al. 1992). Small amounts of methylmercury also may be produced abiotically in 

sediment (Falter and Wilken, 1998). Maximum methylmercury production occurs at the oxicanoxic boundary in sediment, usually several centimeters below the surface. Although less 

common, methylmercury also may be formed in anaerobic water (Regnell et al., 1996 and 

2001). In this case, mercury-methylating microbes move from the sediment to the overlying 

water and the resulting methylmercury becomes available to the biotic community when aerobic 

and anaerobic waters mix. Methylmercury is a byproduct of the metabolism of sulfate-reducing 

bacteria. The amount of methylmercury produced is a function of the amount of active bacteria, 

their available food, and conditions that affect bacterial growth, such as temperature and pH. 

Given conditions and food positive for growth, sulfate-reducing bacteria will produce 

methylmercury even if methylmercury is present in the surrounding environment 

(i.e., methylmercury production is not controlled by chemical equilibrium). 

Demethylation is both a biotic and abiotic process. Both sulfate reducing and methanogen-type 

bacteria have been reported to demethylate mercury in sediment with maximum demethylation 

co-occurring in the same zone where maximum methylmercury production is located (MarvinDiPasquale et al., 2000). Photodegradation of methylmercury in the water column also has 

been observed (Sellers et al., 1996; Byington et al., 2005; Gill, 2008a). While not well studied, 

the rates of both biotic and abiotic demethylation appear important in controlling net 

methylmercury concentrations in aquatic ecosystems (Sellers and Kelly, 2001; MarvinDiPasquale et al., 2000). 

Factors controlling sediment methylmercury production have been the subject of intense 

scientific research (for reviews see Wiener et al., 2003b and Benoit et al., 2003). Sediment 

factors and landscape events important in net methylmercury production include: 

• Sulfate and pH concentration of the overlying water (Gilmour et al., 1998; 

Miskimmin et al., 1992; Krabbenhoft et al., 1999); 

Delta Methylmercury TMDL Report 23 April 2010 
• Percent organic content of the sediment (Krabbenhoft et al., 1999; Miskimmin et al., 

1992; Hurley et al., 1998; Heim et al., 2003; Slotton et al., 2003); 

• Creation of new water impoundments (Verdon et al., 1991; Bodaly et al., 1997); 

• Amount and kind of inorganic mercury present in the sediment (Krabbenhoft et al., 1999; 

Bloom, 2003); and 

• Amount of permanent or seasonally flooded wetland in a watershed (Krabbenhoft et al., 

1999; Brumbaugh et al., 2001; St Louis et al., 1994 and 1996; Hurley et al., 1995). 

Sediment factors and landscape events important in net methylmercury loss in the Delta 

include: 

• Deposition of particle-bound methylmercury in the water column; and 

• Photodegradation of methylmercury in the water column. 

The significance of deposition and photodegradation in the Delta were reported in the second 

set of CALFED mercury reports released in 2008 (Stephenson et al., 2008; See Section 3.6) 

The level of oxygenation in a water body also affects methylmercury production. The San 

Francisco Bay Regional Water Quality Control Board required the Santa Clara Water District to 

test methylmercury controls in three of its reservoirs and to report monitoring results 

(SFBRWQCB, 2008). Levels of methylmercury in the water column of Lake Almaden 

decreased significantly after the Santa Clara Valley Water District installed solar-powered water 

circulators (SCVWD IMC, 2009). Aeration has not been specifically tested in the Delta as a 

measure to reduce methylmercury concentrations, but may be effective in some situations, such 

as dredged material settling ponds. 

The following sections focus on potentially controllable processes for within-channel 

methylmercury sources (e.g., wetlands and open-water habitat). Additional point and nonpoint 

sources are described in Chapters 6, 7 and 8. The organic content of the sediment and the pH 

of the overlying water are not discussed further as neither appears controllable in the Delta. 

3.1 Sulfate 

Sulfate is used by sulfate reducing bacteria as the terminal electron acceptor in the oxidation of 

organic material. Sulfate additions have been observed to both stimulate (Gilmour et al., 1992; 

King et al., 2002) and inhibit (Benoit et al., 1999; Gilmour et al., 1998) methylmercury 

production. Addition of sulfate is predicted to stimulate methylmercury production when it is 

limiting. In contrast, sulfate amendments may inhibit production when excess sulfide is present. 

Sulfide is the primary byproduct in the reduction of sulfate and increasing sulfide concentrations 

may cause inhibition by either decreasing the amount of neutrally charged dissolved mercurysulfide complexes9

 (Benoit et al., 1999 and 2001, but see Kelley et al., 2003, for conflicting 

results) or by precipitating insoluble mercuric sulfide (Compeau and Bartha, 1985). 

 

9

 Dissolved, neutrally charged mercury is the only form that readily crosses microbial cell membranes. 

Delta Methylmercury TMDL Report 24 April 2010 
Two factors influencing sulfate concentrations in the Delta are the water quality objectives for 

electrical conductivity (EC) and the ratio of San Joaquin River to Sacramento River water. Both 

are controllable water quality factors and result from water management decisions made by the 

State of California. Table 3 of Water Rights Decision 95-1WR stipulates maximum ambient 

electrical conductivity values for various locations in the Delta by month and water year type 

(SWRCB, 1995). Electrical conductivity in the Delta is primarily a function of freshwater outflow 

and seawater intrusion.10 Water Right Decision 95-1WR regulates electrical conductivity by 

specifying both the amount of freshwater outflow and the amount of water exported to southern 

California. For example, during 2000-2001, the 2 o/oo salinity level11 in ambient bottom water 

was located as far seaward as the City of Martinez in March 2000, but migrated as far upstream 

as Rio Vista in the summer of 2001 (Foe, 2003). The upstream movement of the salinity field 

had the effect of increasing sulfate concentrations in western Delta water by about ten-fold. 

Sulfate concentrations are about seven times higher in the San Joaquin River than in the 

Sacramento River. At present, the San Joaquin River is almost entirely diverted out of the Delta 

by way of Old River and Grantline Canal for export to southern California via the state and 

federal pumping facilities near Tracy. This reduces the proportion of San Joaquin River water in 

much of the southern and central Delta and allows intrusion of Sacramento River water with 

lower sulfate concentrations. The Record of Decision for the CALFED Bay-Delta Program 

committed the State to evaluate and, if practical, begin construction of a series of permanent, 

operable barriers in the southern Delta to better control the routing of San Joaquin River water 

(CALFED Bay-Delta Program, 2004b). An indirect consequence of the permanent barriers is 

that their operation will determine sulfate concentrations in much of the central and southern 

Delta. 

Sulfate amendment studies need to be undertaken with sediment collected throughout the year 

from the southern, central and western Delta to determine whether the sulfate concentration in 

the overlying water affect methylmercury production in sediment. Results of these experiments 

can be considered when evaluating how to manage the permanent, operable barriers in the 

southern Delta and when considering water right decisions to modify the location of the salinity 

field in the Delta. 

3.2 New Water Impoundments 

The creation of new water impoundments has been found to stimulate sediment microbial 

activity and to increase methylmercury concentrations in sediment, water and biota 

(Verdon et al., 1991; Bodaly et al., 1997). The State of California has a growing population and 

a limited water supply for municipal and agricultural use. One alternative under evaluation is the 

construction of additional reservoir storage. The Record of Decision for the CALFED Bay-Delta 

Program directs agencies and local interests to continue to evaluate five surface water storage 

options to improve water management (CALFED Bay-Delta Program, 2004a). These include 

north of Delta off-stream storage, in-Delta storage, Shasta Lake expansion, Los Vaqueros 

 

10 Sulfate concentrations in the Sacramento and San Joaquin Rivers varied between 6-14 and 42-108 mg/l in 2000 

and 2001 (Foe, 2003) while full strength seawater is 2,700 mg/l (Parsons and Takahashi, 1973). 11 Salinity is generally reported in terms of parts per thousand (abbreviated o/oo), the number of pounds of salt per 

1,000 pounds of water. 

Delta Methylmercury TMDL Report 25 April 2010 
Reservoir expansion and upper San Joaquin storage. Environmental planning for each project 

is underway and should evaluate the potential of each new facility to increase downstream 

methylmercury concentrations in the Delta. 

3.3 Sediment Mercury Concentrations 

Methylmercury production has been found to be a function of the total mercury content of the 

sediment. Methylmercury concentrations12 adjusted for the organic content of the sediment 

increased logarithmically with increasing total mercury concentration in a study of 106 sites from 

21 basins across the United States (Krabbenhoft et al., 1999). The slope of the relationship 

was linear to approximately 1 mg/kg total mercury before commencing to asymptote. Similar 

linear relationships have been observed in the Delta between methyl and total mercury 

concentrations in sediment (Table 3.1). The statistical significance of the correlation increases 

when data from one land use type (e.g., marshes) are used. This implies that methylation rates 

may also be a function of habitat type. The results are consistent with laboratory experiments 

where increasing concentrations of inorganic mercury were amended into sediment and the 

evolution of methylmercury monitored. The efficiency of the conversion of total to 

methylmercury was linear to about 1 mg/kg before commencing to level off (Bloom, 2003; 

Rudd et al., 1983). 

Mercury concentrations in fish at contaminated sites decline after control measures are 

instituted to reduce incoming mercury loads (Table 3.2). Most sites studied to date are 

industrial facilities that discharge to fresh water and have operated for relatively short periods.13 

The initial decrease in fish tissue concentration near the source of contamination is often fast 

with about a 50% decline in the first five to ten years. However, after a rapid initial decrease, 

concentrations tend to stabilize with little, if any, subsequent decline (Turner and Southworth, 

1999; Takizawa, 2000; Lodenius, 1991; Lindestrom, 2001; Francesconi et al., 1997). The new 

equilibrium value is usually higher than in adjoining uncontaminated waterways and is also often 

greater than what is recommended as safe for human consumption (Turner and Southworth, 

1999; Parks and Hamilton, 1987; Lodenius, 1991; Lindestrom, 2001; Francesconi et al., 1997; 

Becker and Bigham, 1995). The reasons are unclear but may be because small amounts of 

mercury are still entering from terrestrial sources (Turner and Southworth, 1999) or because of 

difficulties in bringing sediment concentrations down to background levels (Francesconi et al., 

1997; Jernelov and Asell, 1975). If contamination has spread to areas more distant than the 

immediate facility, then reductions in fish tissue concentrations are much slower 

(Southworth et al., 2000). Absent from the literature are reports on remediation of pollution from 

mercury mining. The magnitude and duration of mercury and gold mining in California, coupled 

with the extensive distribution of contamination, will likely make recovery much slower than at 

industrial sites (Table 3.2). 

 

12 Radiotracer experiments in Florida Everglade sediment demonstrate that methylmercury production is positively 

correlated with bulk sediment methylmercury concentrations (Gilmour et al., 1998). Moreover, the spatial pattern of 

methylmercury production was strongly correlated with aqueous and biotic concentrations, suggesting that surficial 

sediment concentrations could be used as an analog for in situ methylmercury production and flux into the 

overlying water. Bulk methylmercury sediment concentrations are now widely used as an index of methylmercury 

production (Krabbenhoft et al., 1999; Bloom et al., 1999 and 2003; Heim et al., 2003; Slotton et al., 2003; Conaway 

et al., 2003; Benoit et al., 1999). 13 One to two decades. 

Delta Methylmercury TMDL Report 26 April 2010 
Delta Methylmercury TMDL Report 27 April 2010 

As part of the mercury control program for San Francisco Bay, San Francisco Water Board staff 

established a goal for Bay sediment of 0.2 mg/kg mercury and assigned Central Valley outflows 

a total mercury load reduction of 110 kg per year to achieve it (Johnson and Looker, 2004; 

SFBRWQCB, 2006). Waterborne mercury and total suspended sediment loads in the Delta’s 

tributaries are summarized in Chapter 7. Initial management actions of the Delta methylmercury 

TMDL could consider controlling mercury from watersheds with high methylmercury 

concentrations in fish, high mercury to suspended sediment ratios and large areas of 

downstream marsh. The initial goal would be to meet the San Francisco Water Board’s goal of 

110 kg total mercury reduction per year, but additional load reductions eventually may be 

needed to achieve compliance with the recommended fish tissue methylmercury targets for the 

Delta (Chapter 4). 

Table 3.1: Field Studies Demonstrating a Positive Correlation Between Total Mercury and 

Methylmercury in Freshwater Surficial Sediment 

Location (a) R2 P-Value Comments Author 

Sacramento-San Joaquin Delta Estuary 0.2 <0.01 All habitats in Delta combined. Heim et al., 2003 

Sacramento-San Joaquin Delta Estuary 0.52 <0.001 Only marsh habitats. Heim et al., 2003 

Sacramento-San Joaquin Delta Estuary 0.37 <0.001 Comparisons inside and outside 

of flooded Delta Islands. Slotton et al., 2003

Elbe River 0.69 <0.0001 Germany. Hintelmann & 

Wilken, 1995 

Patuxent River Estuary 0.61 <0.05 Sub embayment of 

Chesapeake Bay. 

Benoit et al., 

1998 

National Survey 0.62 <0.0001 

Log/log relationship normalized to 

percent organic carbon at 106 

sites in 21 basins across the 

United States. 

Krabbenhoft et al., 

1999 

Lake Levrasjon 0.64 <0.05 Southern Sweden. Regnell & Ewald, 

1997 

(a) The majority of the sediment in each study had a mercury content less than 1 ppm. 
Table 3.2: Change in Fish Tissue Mercury Concentration After Initiation of Source Control. 

Location Mercury Source Biotic Change Control Measures 

Oak Ridge National 

Laboratory, Tennessee Weapons Facility 

Sunfish at discharge point declined from 2 to 1 mg/kg in 5 yrs; half 

mile downstream sunfish declined from 0.9 to 0.7 mg/kg in 9 yrs; no 

change in tissue 2 and 5 miles downstream. 

Reduced discharge, excavated portio

flood plain. 

Lake St. Clair, Michigan Two Chloralkali Plants Walleye fish declined from 2.3 to 0.5 mg/kg in 25 yrs Reduced/eliminated discharge 

Abbotts Creek, North 

Carolina 

Battery 

Manufacturing plant Fish declined from 1 to 0.5 mg/kg in 11 yrs 

Treated groundwater, 

reduced/eliminated discharge, remo

contaminated soil, natural sedimen

burial 

Saltville, Virginia Chloralkali Plant Rockfish declined from 3.5 to 1 mg/kg in 20 yrs 

River sediment dredged, rock botto

grouted, rip-rap river bank, pond 

seepage treated with activated carb

Howe Sound, British 

Columbia, Canada Chloralkali Plant Dungeness crab declined from 2 to 0.2 mg/kg in 5 yrs. No subsequent change Reduced/eliminated discharge, trea

groundwater 

Little Rock Lake, 

Wisconsin 

Atmospheric 

deposition Yellow Perch declined 30% in 6 yrs Reduced atmospheric mercury input 

60%. 

Minimata, Japan Chloralkali Plant Fish declined from 9.0 to 0.4 mg/kg in 8 yrs; no further change. Eliminated discharge; dredged an

disposed of sediment. 

Clay Lake, Ontario, 

Canada 

A chloralkali plant 

and a wood pulp mill. 

Walleye fish declined from 15.1 to 2.0 mg/kg in 20 yrs. Background 

concentration is 0.6 mg/kg. 

Eliminated discharge; natural burial 

contaminated sediment 

Ball Lake, Ontario, 

Canada (downstream of 

Clay Lake) 

Same as above Walleye fish declined from 2.0 to 1.4 mg/kg in first 5 yrs. Northern Pike from 5.1 to 1.8 mg/kg. No change in Lake Whitefish. Same as above 

Lake Kirkkojarvi, Finland Phenylmercury in slimicide in pulp mill 4 and 1-kg Northern Pike declined from 3.6 to 2.1 and from 1.5 to 0.8 mg/kg in 20 yrs. All reductions happened in first 10 yrs. Background concentration in 1-kg pike is 0.4 mg/kg. Reduced discharge, natural buria

Lake Vanern, Sweden Chloralkali Plant 

5-yr old Northern Pike declined from 1.4 to 0.6 mg/kg in 25 yrs. 

Most of decrease occurred in first 10-15 yrs. Background 

concentrations in Pike are 0.4 mg/kg 

Reduced/eliminated discharge, natu

burial 

Princess Royal Harbor, 

Australia (Marine water) 

Superphosphate 

Processing Plant 

Mercury in 8 marine fish species declined by about 50% in 9-yrs. 

Most of decrease happened in first 4-yrs. Tissue concentrations are 

still about twice background. 

Eliminated discharge, natural buria

Onondaga Lake, New 

York 

Municipal and 

industrial discharge 

Mercury in six fish species declined by 60 to 80 % in 22 yrs. Tissue 

concentrations are still about twice background. Eliminated discharge, natural buria

North Carolina, Quebec, 

Finland, Manitoba, 

Labrador and 

Newfoundland 

Reservoir creation Fish tissue levels declined to normal after 3 to 30 years. None 

Delta Methylmercury TMDL Report 28 
3.4 Forms of Mercury 

There are primarily two different forms of mercury transported into the Delta with potentially 

different methylation rates. The first form is mercury mine waste from the Coast Range. Most 

of this material is thought to be mercuric sulfide, cinnabar and metacinnabar (Bloom, 2003). 

Mercury mine waste enters the Delta from mine-impacted coast range creeks such as Putah 

and Cache Creeks. The second form is elemental mercury lost from placer and hardrock gold 

mining operations in the Sierra Nevada Mountains. Elemental mercury enters the Delta in 

Sacramento, Mokelumne and San Joaquin River water that drains from the northern and 

southern gold fields. [Additional sources of mercury are described in Chapter 7.] 

Mercury from gold mining appears to be more biologically available than material from mercury 

mines. The evidence is twofold. First, Frontier Geosciences conducted a 1-year microcosm 

incubation study with both gold and mercury mine waste to determine the relative methylation 

efficiency of each (Bloom, 2003). Mercury from gold mining was found to have the higher 

methylation rate. Second, the ratio of methyl to total mercury in natural sediment is assumed to 

be a field measure of methylation efficiency (Gilmour et al., 1998; Krabbenhoft et al., 1999; 

Bloom et al., 1999 and 2003). Heim and others (2003) collected sediment at multiple locations 

in Cache Creek (representative of mercury mine waste) and the Cosumnes River 

(representative of gold mine material) on three occasions (October 1999, May 2001 and 

October 2001) to determine methyl and total mercury concentrations and methylation 

efficiencies. The highest methyl to total mercury ratios were consistently observed in 

Cosumnes River material. These results are consistent with the conclusions of Bloom (2003) 

and suggest that floured elemental mercury from gold mining in the Sierra Nevada is more 

readily methylated than is cinnabar from the Coast Range. 

Heim and others (2003) also collected sediment samples at multiple locations in Cache Creek. 

The ratio of methylmercury to total mercury increased with increasing distance from the mercury 

mining districts. The authors speculate that diagenic weathering-type processes are changing 

the form of the mercury and increasing its methylation efficiency as the material is slowly 

transported away from the mines. The precise mechanisms are not known but may include the 

formation of soluble polysulfide complexes (Paquette and Heltz, 1995) and dissolution of 

cinnabar by humic and fulvic acids (Wallschläger et al., 1998; Ravichandran et al. 1998). Both 

processes should increase the efficiency of the conversion of inorganic to organic mercury. No 

similar weathering type experiments have been conducted on Sierra Nevada gold mine-derived 

mercury. The Cache Creek findings suggest that there is currently insufficient understanding of 

mercury weathering processes to justify developing control programs that preferentially target 

controlling gold-mine waste material. 

3.5 Wetlands 

Research in the Delta and elsewhere has found that wetlands are sites of efficient 

methylmercury production (Slotton et al., 2003; Heim et al., 2003; St. Louis et al., 1994, 1996; 

Gilmour et al., 1998). In fact, one of the best predictors of methylmercury concentrations in 

water and in biota is the amount of wetland present in upstream watersheds (Krabbenhoft et al., 

Delta Methylmercury TMDL Report 29 April 2010 
1999; Wiener et al., 2003b). The Record of Decision for the CALFED Bay-Delta Program 

commits it to restore 30,000 to 45,000 acres of fresh, emergent tidal wetlands, 17,000 acres of 

fresh, emergent nontidal wetlands, and 28,000 acres of seasonal wetlands in the Delta by 2030 

(CALFED Bay-Delta Program, 2000b). This is a total of 75,000 to 90,000 acres of additional 

seasonal and permanent wetlands in the Delta, which represents about a three to four times 

increase in wetland acreage from current conditions. Many of the proposed restoration sites are 

downstream of mercury-enriched watersheds. Marsh restoration efforts below mercury 

enriched watersheds are proposed for the following locations: Yolo Bypass downstream of 

Cache and Putah Creeks; Dutch Flats downstream of the Mount Diablo Mercury mine in the 

Marsh Creek watershed; and Staten Island and the Cosumnes River Wildlife Refuge near the 

confluence of the Cosumnes River and Mokelumne River. Extensive restoration efforts in the 

Delta have the potential to increase methylmercury exposure for people and wildlife. This 

potentially significant adverse environmental impact was identified in CALFED’s programmatic 

ROD’s CEQA evaluation. 

Even though much of the research has found that wetlands act as sources of methylmercury, 

recent data indicate that some wetlands may act as net methylmercury sinks. Table 3.3 

provides a summary of methylmercury production characteristics from different types of 

wetlands in the Delta region. In addition, a technical review of the June 2006 TMDL Report 

described a study conducted in southern Florida, in which different wetland and open water 

sites were found to contain varying levels of methylmercury (Tetra Tech, Inc., 2006). More 

research is needed to understand the processes that affect a wetland’s methylmercury 

production, so that wetland restoration can occur with minimal methylmercury production 

increases. 

Table 3.3: Summary of Wetland Methylmercury Production Characteristics.

Watershed Site (a) Wetland Type MeHg Characteristics (b)

Twitchell Island (1) 2 Permanent (test ponds) Both sources 

Browns Island (2) Permanent, tidal Small source 

Sycamore Slough (3) Permanent, tidal Sink 

Delta 

Grizzly Island (Suisun Marsh) (4) 2 Seasonal Source 

Anderson Marsh (5) Permanent Source 

Cache Creek 

Cache Creek Nature Preserve (6) Permanent Source 

2 Permanent Both neutral 

Mud Slough San Luis Wildlife Refuge (7) 

6 Seasonal All sources 

First Mallard Branch (interior marsh) (3) Permanent, tidal Source 

Suisun Marsh 

Suisun Slough (mouth) (3) Permanent, tidal Sink 

(a) Study citations: (1) Sassone et al., 2006; Sassone et al., 2008 (2) Fleck et al., 2007; (3) Heim et al., 2007; (4) Stephenson et al., 

2008; (5) CVRWQCB, unpublished data; (6) Slotton and Ayers, 2001; (7) Stephenson et al., 2007. 

(b) Wetlands that act as net producers of methylmercury are noted as “sources”; wetlands that act as sinks for methylmercury 

(e.g., more methylmercury is imported than exported) are noted as “sink”; and wetlands that apparently acted as neither a source 

nor sink for methylmercury are noted as “neutral”. 

Delta Methylmercury TMDL Report 30 April 2010 
3.6 Methylmercury Loss by Sedimentation and Photodemethylation 

As water moves across the Delta from the Sacramento River to the pumps, settling of 

methylmercury bound to particles reduces aqueous methylmercury concentrations (Stephenson 

and Bonnema, 2008). Losses of methylmercury and particles were shown in samples collected 

as water from both the Sacramento and San Joaquin Rivers moved through the Delta 

(Heim et al., 2008). The transect sampling by Heim and colleagues tracked the two largest 

sources of water entering the Delta and identified losses at two points: downstream of the 

convergence of the Sacramento River with Cache and Steamboat Sloughs and entry of San 

Joaquin River water into the San Joaquin Deep Water Ship Channel. The methylmercury loss 

in the San Joaquin River was not observed in some winter and spring sampling events. Data 

collected during the recent CalFed mercury project (Heim et al., 2008; Foe et al., 2008) were 

used in a particle transport model that demonstrated methylmercury movement in multiple flow 

paths across the Delta (Stephenson et al., 2008b). Methylmercury loss rates due to 

photodemethylation and particle settling varied by flow path and season. 

Methylmercury loads from in-channel sources such as wetlands, ponds, and settling basins, as 

well as retention basins in urban areas, may be able to be controlled by enhancing their 

sediment trapping efficiency. During stakeholder meetings in 2009, entities responsible for 

methylmercury from managed wetlands and irrigated agriculture began gathering information 

and considering possible ways to enhance sedimentation of methylmercury. Ideas that could be 

investigated during studies in the first phase of the Delta mercury control program include: 

adding a sill or specific vegetation to trap sediment, creating small settling basins within 

drainage canals, and managing flow and depth within a pond or wetland system to maximize 

settling (Stephenson, 2009). 

The results of the particle transport modeling (Stephenson et al., 2008b) could lead to changes 

in how the Delta subareas are delineated (see Section 2.2.2 in Chapter 2). For example, during 

a model run for August 2005 (Stephenson, 2009, video provided through pers. comm.), the 

particle tracking model indicates the San Joaquin River subarea could be re-delineated to 

include more of the Central Delta subarea, and the Sacramento River subarea could be redelineated to include a portion of the southern Yolo Bypass subarea. If funding can be 

acquired, staff hopes to work with the particle transport model study authors to evaluate a 

variety of typical hydrographic periods and, if needed, re-delineate the Delta subareas to better 

reflect the water and sediment sources that drive water and fish methylmercury concentrations 

in different Delta areas. 

Delta Methylmercury TMDL Report 31 April 2010 
Key Points 

• The problem with mercury in the Delta’s aquatic ecosystems can be defined as biotic 

exposure to methylmercury. Therefore, decreasing biotic exposure to methylmercury is the 

ultimate goal of the Delta methylmercury TMDL and implementation program. 

• The implementation plan should focus on sources and processes that are potentially 

controllable in the Delta. Potentially controllable sediment factors and landscape events 

important in net methylmercury production include: water rights salt standards in the Delta; 

creation of new water impoundments; amount of inorganic mercury present in the sediment; 

and management of permanent or seasonally flooded wetland in a watershed. 

Delta Methylmercury TMDL Report 32 April 2010 
4 NUMERIC TARGETS 

Water quality targets for mercury in fish were calculated to protect beneficial uses of the water 

and aquatic resources of the Delta. The targets are intended to reduce the risks to humans and 

wildlife that consume fish and other aquatic organisms from the Delta that contain 

methylmercury. This chapter first describes the derivation of species-specific targets based on 

a suite of fish types to protect humans and wildlife. The Central Valley Water Board staff 

proposes three targets for the protection of human and wildlife health: 0.24 mg/kg (wet weight) 

in muscle tissue of large trophic level four (TL4) fish such as bass and catfish; 0.08 mg/kg (wet 

weight) in muscle tissue of large TL3 fish such as carp and salmon; and 0.03 mg/kg (wet 

weight) in whole trophic level 2 and 3 fish less than 50 mm in length. In addition, staff proposes 

an implementation goal of 0.24 mg/kg methylmercury, wet weight, in standard 350-mm 

largemouth bass. As described in Chapter 5, this implementation goal can be linked to aqueous 

methylmercury to develop an implementation goal for methylmercury in unfiltered ambient 

water, which in turn can be used to determine methylmercury source reductions needed to 

achieve the proposed targets for methylmercury in fish. 

In addition to addressing sources of methylmercury to the Delta, the Delta mercury control 

program addresses total mercury sources to the Delta and San Francisco Bay. The San 

Francisco Bay TMDL assigns a load reduction of 110 kg per year from the Central Valley 

(Johnson and Looker, 2004; SFBRWQCB, 2006). As described in later chapters of this report, 

the mercury control program for the Delta is designed to achieve the total mercury load 

reduction required by the San Francisco Water Board, as well as to maintain compliance with 

the USEPA’s CTR for total mercury in freshwater sources and to limit total mercury sources to 

the Delta to ensure that methylmercury levels in fish do not increase in the future. 

4.1 Definition of a Numeric Target 

Numeric targets are the specific goals for the TMDL that will enable the protection of the 

beneficial uses of the Delta and San Francisco Bay. The development of numeric targets 

involves the following elements: 

• Identification of the target media and the basis for using the selected target media to 

interpret or apply applicable water quality standards. 

• Identification of target levels for the selected target media and the technical basis for the 

target levels. 

• Comparison of historical or existing conditions and desired future conditions for the target 

media selected for the TMDL. 

4.2 Clean Water Act 303(d) Listing and Beneficial Use Impairment 

The Office of Environmental Health Hazard Assessment issued health advisories 

recommending that consumers limit their consumption of striped bass and sturgeon from the 

Delta and Bay because of high methylmercury tissue concentrations (Section 2.4.1). The fish 

Delta Methylmercury TMDL Report 33 April 2010 
advisory resulted in the Central Valley and San Francisco Water Boards listing the Bay-Delta 

Estuary as impaired. 

By definition, an impaired water body does not support all of its designated beneficial uses. 

Existing and potential beneficial uses are listed in Table 2.3 in Chapter 2. The Delta provides 

habitat for warm and cold water species of fish and the aquatic communities associated with 

them. In addition, the Delta and associated riparian areas provide valuable wildlife habitat. 

Beneficial uses that are impaired due to high mercury levels include commercial and sport 

fishing and wildlife habitat. 

4.3 Selection of the Type of Target for the Delta 

4.3.1 Fish Tissue 

Measurements of mercury in the target media should be able to assess fairly directly whether 

beneficial uses are being met. Several media for numeric targets were considered, including 

sediment, water column and biota. The major beneficial use of the Delta that is currently unmet 

is its use as a safe fishery for humans and wildlife. A target of mercury in fish tissue was 

determined to be the most appropriate because it provides the most direct assessment of 

fishery conditions and improvement. Fish tissue data have been collected between 1969 and 

2002 in the Delta. Existing data for fish species consumed by humans and wildlife provide a 

baseline against which future improvements can be measured. 

Targets are developed for methylmercury in fish tissue because it is the most toxic form of 

mercury. It is also the form to which humans and wildlife may be exposed in the Delta at levels 

sufficient to cause adverse effects. The cost for methylmercury analysis is greater than that for 

total mercury; therefore, most data available are for total mercury in fish tissue. Independent 

research demonstrates that most mercury (85-100%) in fish muscle is methylmercury (Becker 

and Bigham, 1995; Slotton et al., 2004). For the purposes of the TMDL, Central Valley Water 

Board staff assumes that all the mercury measured in Delta fish is methylmercury. 

4.3.2 San Francisco Bay Numeric Target 

The Delta TMDL is structured to meet the San Francisco Bay mercury TMDL’s total mercury 

allocation for Central Valley outflows to the Bay. San Francisco Water Board staff developed a 

target for San Francisco Bay sediment mercury concentration of 0.2 mg/kg and assigned the 

Central Valley a five-year average total mercury load allocation of 330 kg/yr at Mallard Island or 

a decrease of 110 kg/yr in mercury sources to the Delta. The 2004 San Francisco Bay mercury 

TMDL staff report provides a detailed derivation of the San Francisco Bay sediment target and 

allocation for the Central Valley (Johnson and Looker, 2004; SFBRWQCB, 2006). Strategies for 

reducing the total mercury loading to San Francisco Bay are discussed in Chapter 8 in this 

TMDL report and Chapter 4 in the draft Basin Plan Amendment staff report. 

Delta Methylmercury TMDL Report 34 April 2010 
4.3.3 Water Criteria 

The California Toxics Rule (CTR) mercury criterion applies to the Delta (see Section 2.3.2.2). 

This criterion of 50 ng/l total recoverable mercury in water is intended to protect the health of 

humans consuming contaminated organisms and drinking water. The CTR value may not be 

sufficiently protective of humans consuming fish from the Delta because of the low 

bioconcentration factors used to derive the CTR value. Central Valley Water Board staff 

considers fish tissue targets to be more stringent than the CTR criterion.14 Although the CTR 

criterion may be less protective than the fish tissue targets discussed below, the TMDL was 

designed to comply with the CTR mercury criterion. Compliance with the CTR criterion through 

the TMDL is discussed in the total mercury source assessment (Chapter 7) and total mercury 

limits (Chapter 8) sections of this report. 

4.4 Fish Tissue Target Equation and Development 

Key variables that are incorporated into the calculation of fish tissue targets are: 

• Acceptable daily dose level of methylmercury; 

• Body weight (bwt) of the consumer; 

• Trophic level or size of fish consumed; and 

• Rate of fish consumption. 

These components can be related using a basic equation (OEHHA, 2000; USEPA, 1995c) as 

follows. 

Equation 4.1: 

Safe daily intake * Consumer’s body weight = Acceptable level of mercury in fish tissue 

 Consumption rate 

At or below the safe daily intake of methylmercury, consumers are expected to be protected 

from adverse effects. An acceptable intake level is also called a reference dose (RfD). An RfD 

is expressed as an average daily rate (micrograms of mercury per kilogram body weight per 

day) of mercury intake. In general, an RfD is calculated by using studies of exposure in specific 

populations to determine a threshold level of exposure below which adverse effects did not 

occur. The threshold level is then divided by uncertainty factors that lower the value to the final 

reference dose. Uncertainty factors account for differences in metabolism and sensitivity 

between individuals, lack of toxicity information in available studies, or other unknowns. 

In the calculation of its recommended methylmercury criterion to protect human health, USEPA 

added a relative source contribution (RSC) component to the equation to account for 

methylmercury from other sources (USEPA, 2001). Humans are exposed to methylmercury 

 

14 The weighted average practical bioconcentration factor (PBCF) used to develop the CTR mercury criterion is 

7342.6 (USEPA, 2000b). For the Delta, bioaccumulation factors (BAF) for large trophic 4 fish are in the range of 

50,000 to 300,000. These BAFs are the ratios of mercury in fish to the concentration of total recoverable mercury 

in water. The Delta bioaccumulation factors indicate that piscivorous fish species in the Delta accumulate higher 

concentrations of mercury than USEPA’s PBCF. 

Delta Methylmercury TMDL Report 35 April 2010 
from commercial fish as well as locally caught fish. Human intakes of methylmercury from all 

other sources (air, drinking water, soil, and foods other than fish and seafood) are considered 

negligible. The RSC represents that portion of methylmercury exposure that will not be 

controlled by cleanup actions directed to a particular water body. Because piscivorous wildlife 

species are assumed to obtain all of their fish or other aquatic prey from the local water body, 

no RSC adjustment is used for the wildlife calculations. As with humans, the direct intake of 

methylmercury by piscivorous wildlife from air or water is negligible relative to intake from fish 

and aquatic organisms (USEPA, 1997a). 

The consumption rate can be separated into rates of consumption of fish from each trophic 

level. Adjusting for multiple consumption rates and the RSC, the basic equation appears as 

follows. 

Equation 4.2: 

(Safe intake – RSC) * body weight = Acceptable level of mercury 

 (CRateTL2 + CRateTL3 + CRateTL4) in Delta fish tissue

Where: CRateTL2 = consumption rate of fish from Trophic Level 2 

CRateTL3 = consumption rate of fish from Trophic Level 3 

CRateTL4 = consumption rate of fish from Trophic Level 4 

Safe levels of methylmercury in fish tissue that protect wildlife are presented first in this report, 

followed by the human health targets. The order of presentation and in-depth discussion of 

wildlife methodology are not intended to suggest greater importance of wildlife targets relative to 

human health targets. Rather, wildlife targets are discussed first because the safe fish tissue 

levels are based on average consumption rates that are assumed to be constant. Human 

consumption rates, however, vary widely by individual. For targets to protect human 

consumers, consumption rate options are incorporated into the calculations. 

4.5 Wildlife Health Targets 

Birds and mammals most likely at risk for mercury toxicity are primarily or exclusively 

piscivorous. Those identified for the Delta are: American mink, river otter, bald eagle, 

kingfisher, osprey, western grebe, common merganser, peregrine falcon, double crested 

cormorant, California least tern, and western snowy plover15 (USEPA, 1997a; CDFG, 2002). 

Bald eagles, California least terns and peregrine falcons are listed by the State of California or 

by the USFWS as either threatened or endangered species. The Delta is a foraging and 

possible wintering habitat for bald eagles (USFWS, 2004). California least terns also forage in 

the Delta. There is at least one nesting colony of these terns within the Delta (USFWS, 2004). 

 

15 The CDFG California Wildlife Habitat Relationships database also reports observations of brown pelicans and 

clapper rails in the Delta. Both of these species are federally listed as endangered and depend on the aquatic food 

web. However, it has been confirmed that brown pelicans and clapper rails prefer saltwater habitats and are only 

occasional visitors to the Delta regions as discussed in this TMDL (Schwarzbach, 2003; CDFG, 2005). Peregrine 

falcon are included because they consume piscivorous waterfowl. 

Delta Methylmercury TMDL Report 36 April 2010 
Delta Methylmercury TMDL Report 37 April 2010 

Although most of the Delta habitat is unlike that preferred by peregrine falcons for nesting, 

several peregrine falcon pairs have nested on bridges in the area (Linthicum, 2003). 

Acceptable fish tissue mercury levels for wildlife species can be calculated using daily intake 

levels, body weights and consumption rates. Parameters needed to estimate daily 

methylmercury exposures and safe levels of methylmercury in prey for wildlife are given in 

Table 4.1. Mercury studies conducted in the laboratory and field are used to derive RfD for 

birds and mammalian wildlife. The following section uses these RfDs to calculate fish tissue 

targets to protect the health of wildlife in the Delta. 

4.5.1 Reference Doses, Body Weights & Consumption Rates 

The reference dose for mammalian wildlife species of 0.018 mg methylmercury/kg bwt/day is 

based on studies in which mink were fed methylmercury at varying doses and evaluated for 

neurological damage, growth and survival (USEPA, 1995a; USEPA, 1997b). Studies of mallard 

growth and reproduction following methylmercury exposure were used to determine a 

methylmercury reference dose for birds of 0.021 mg/kg bwt/day (USEPA, 1997b). For each of 

reference doses, the lowest toxic dose was divided by three (uncertainty factor) to account for 

differences in species’ and individuals’ reactions to mercury and produce a dose level at which 

harmful effects are not expected (USFWS, 2003). 

Average body weights of adult females are used because the most sensitive endpoints of 

methylmercury toxicity are related to reproductive success. The USFWS provided guidance to 

Central Valley Water Board staff regarding the species of concern and their exposure 

parameters (USFWS, 2002, 2003 and 2004). 

4.5.2 Safe Methylmercury Levels in Total Diet 

Fish tissue mercury levels that would result in methylmercury intakes by piscivorous wildlife at 

or below safe intake levels are calculated in two steps. First, safe levels of methylmercury in the 

total diet of each wildlife species are calculated (Table 4.2). The total diet safe level represents 

the concentration of methylmercury, as an average in all prey consumed, needed to keep the 

organism’s daily intake of methylmercury below the reference dose. Total diet safe levels were 

calculated using the exposure parameters for wildlife species and Equation 4.1. In the second 

step, the total diet safe level is translated into protective levels of methylmercury in various 

components of an organism’s diet (Table 4.3). An example calculation of the total safe diet 

level for mink is shown below:

Mammalian reference dose * Mink body weight = Total diet safe level 

Mink fish consumption rate 

18 μg MeHg/kg day * 0.60 kg = 0.077 μg MeHg/g total diet (0.077 mg/kg) 

 140 g/day 
Table 4.1: Exposure Parameters for Fish-Eating Wildlife 

Body 

weight (b)

Total 

Food 

Ingestion 

Rate (c)

Trophic 

Level 2 

Aquatic 

Prey 

Trophic 

Level 3 

Aquatic 

Prey 

Trophic 

Level 4 

Aquatic 

Prey 

Piscivorous 

Bird Prey 

Omnivorous 

Bird Prey 

Other 

Foods (d)

Species (a) kg g/day, wet wt g/day, as % of diet g/day, as % of diet g/day, as % of diet g/day, as % of diet g/day, as % of diet g/day, as % of diet 

Mink 0.60 140 - 140 (100%) - - - - 

most pcatch s(USEP

River otter 6.70 1124 - 899 (80%) 225 (20%) - - - 

heterog(USEPmm bufish. 

California 

least tern 0.045 31 - 31 (100%) - - - - mostly 

Western 

snowy plover 0.041 33.3 8.3 (25%) - - - - 25 (75%) 

mainly inverteprey is 

Belted 

kingfisher 0.15 68 - 68 (100%) - - - genera

180 mm 

Common 

merganser (e) 1.23 302 - 302(100%) - - - - most p

1995b; 

Double-crested 

cormorant (f) 1.74 390 - 390 (100%) - - - - genera

360mm 

Western 

grebe (g) 1.19 296 - 296 (100%) - - - - USFWS 

mergan

Bald eagle (h) 5.25 566 - 328 (58%) 74 (13%) 28 (5%) 74 (13%) 62 (11%) 

fish 75-mm (Ja

1995b)

Osprey (i) 1.75 350 - 315 (90%) 35 (10%) - - - fish 100

>200 m

Peregrine 

falcon (j) 0.89 134 - - - 6.7 (5%) 13.4 (10%) 114 (85%) 

Delta Methylmercury TMDL Report 38 
Table 4.1 Footnotes: 

(a) Italics denote species listed as threatened or endangered by state or federal authorities. 

(b) Average female body weights are from Trophic Level and Exposure Analyses for Selected Piscivorous Birds and Mammals 

Volume II (USEPA, 1995b), USFWS (2003, 2004), and as noted below. 

(c) Total food ingestion rates are from USEPA (1995b) and USFWS (2003; 2004) and as noted below. 

(d) Other foods are mainly terrestrial mammal, bird, reptile and invertebrate prey that are presumed to provide negligible amounts 

of methylmercury. 

(e) Merganser body weight and ingestion rate from Schwarzbach and others (2001). 

(f) Cormorant body weight is the average for female birds cited in Hatch and Weseloh (1999). This paper also reports daily 

consumption at 20-25% of body mass. Total ingestion rate of 390 g/day is 22.5% of average female bodyweight. 

(g) Female western grebe body weight from Storer and Nuechterlein (1992). 

(h) Bald eagle parameters provided by the USFWS (2004). Diet of bald eagles in northern California includes fish, mammals and 

birds. Using dietary data from Jackman and others (1999), the USFWS estimated the average proportions of prey types. TL3 

and TL4 fish comprised 58% and 13% of the total bald eagle diet, respectively. Piscivorous birds, such as gulls, grebes, and 

mergansers, comprised approximately 5% of the total diet. An additional 13% of the total diet was comprised of other aquatic 

birds, such as coots, that feed mainly on TL2 organisms. Bald eagles are scavengers and thus consume fish of large sizes 

(Jackman et al., 1999). 

(i) Osprey catch and eat large fish, the majority of which are >200 mm (USEPA, 1995b). In a water body where TL4 sport fish are 

readily available, osprey diet is assumed to be 10% TL4 fish (USFWS, 2002). Prey size is limited to the maximum size that an 

osprey can lift out of water. 

(j) Peregrine falcons eat a wide variety of birds, including grebes, herons, shorebirds, mergansers, gulls and other birds that

accumulate methylmercury from the aquatic food web. USFWS (2004) supports the assumption by Central Valley Water Board 

staff that approximately 15% of peregrine prey in the Delta area is comprised of piscivorous birds. See the appendices of the 

Cache Creek TMDL for Mercury staff report for further analysis of peregrine prey and habitat. 

Table 4.2: Concentrations of Methylmercury in Total Diet to Protect Delta Wildlife Species 

Species 

RfD 

(μg/kg bwt-day)

Body 

Weight

(kg) 

Total Food 

Ingestion Rate

(g/day) 

Safe Methylmercury 

Concentration in Total Diet

(mg/kg in diet) 

Mink 18 0.60 140 0.077 

River otter 18 6.70 1124 0.11 

California least tern 21 0.045 31 0.030 

Western snowy plover 21 0.041 33.3 0.026 

Belted kingfisher 21 0.15 68 0.046 

Common merganser 21 1.23 302 0.086 

Double-crested cormorant 21 1.74 390 0.094 

Western grebe 21 1.19 296 0.084 

Bald eagle 21 5.25 566 0.20 

Osprey 21 1.75 350 0.11 

Peregrine falcon 21 0.89 134 0.14 

Delta Methylmercury TMDL Report 39 April 2010 
Table 4.3: Safe Concentrations of Methylmercury in Fish (mg/kg) by Trophic Level to Protect Wildlife 

Species (a)

TL 2, 

< 50 mm 

TL 2-3, 

50-150 mm 

TL 3, 

150-350 mm

TL 4, 

150-350 mm

TL 3, 

>150 mm 

TL 4, 

>150 mm 

Mink 0.08 

River otter 0.04 0.36 

California least tern 0.03 

Western snowy plover (b) 0.10 

Belted kingfisher 0.05 

Double-crested cormorant 0.09 

Common merganser 0.09 

Western grebe 0.08 

Osprey 0.09 0.26 

Bald eagle (c) 0.11 0.31 

Peregrine falcon (d) (0.17) 

(a) Italics denote species that are listed as threatened or endangered by federal or state authorities. 

(b) The snowy plover safe level should be applied to TL2/3 aquatic invertebrates, such as small clams, crabs, polychaetes and 

amphipods. 

(c) To avoid exceeding the bald eagle wildlife value, safe concentrations must be attained in birds as well as fish eaten by bald 

eagles. The safe levels for average mercury concentrations in omnivorous and piscivorous bird prey are 0.19 and 1.35 mg/kg, 

respectively. Because bald eagles are scavengers, there is no upper size limit on fish eaten by these birds. 

(d) Parentheses denote the TL3 fish level corresponding to the piscivorous bird safe concentration for peregrines. For birds eaten 

by peregrine falcons, the average concentrations should not exceed 2.2 mg/kg in piscivorous bird prey, respectively. 

4.5.3 Calculation of Safe Fish Tissue Levels from Total Diet Values 

Wildlife species consume fish and other aquatic prey from various size ranges and trophic 

levels. In the second step of wildlife target development, safe fish tissue levels are identified for 

different prey classifications. These classifications are termed “trophic level food groups”. 

Table 4.3 shows safe fish tissue concentrations needed by the wildlife species and developed 

for prey within the following trophic level food groups: TL2 fish less than 50 mm in length, 

50-150 mm TL2 and 3 fish, 150-350 mm TL3 fish, and TL4 fish greater than 150 mm. 

In cases in which an organism’s prey is fairly uniform and from one trophic level, the total diet 

safe level becomes the average, safe tissue mercury concentration. For organisms that feed 

from different trophic levels, the proportions of each trophic level in the diet (Table 4.1) are used 

to determine safe tissue mercury levels for each component of the diet. The species whose 

prey falls generally into one size category are mink, California least tern, western snowy plover, 

double crested cormorant, western grebe, kingfisher and common merganser. For these 

species, the total diet safe level becomes the safe fish tissue level matched to the size and 

trophic level of prey consumed. 

Average, safe fish tissue concentrations for kingfisher, cormorant and mink were determined for 

the food group size range of 50-150 mm. Although kingfishers typically consume fish less than 

105 mm in length, they can eat fish as long as 180 mm (Hamas, 1994; USEPA, 1995b). The 

range for cormorant prey is 30 to 400 mm, with most fish eaten being less than 150 mm (Hatch 

and Weseloh, 1999). Most fish caught by mink are in the range of 50-150 mm (USEPA, 1995b). 

Delta Methylmercury TMDL Report 40 April 2010 
As the size ranges of prey caught by these three species are similar, one category of TL2/3 fish 

is appropriate for their protection (USFWS, 2004). 

A second food group of TL3 fish in the range of 150-350 mm incorporates safe fish tissue 

mercury concentrations for prey of common mergansers and western grebes. Most prey caught 

by mergansers is in the range of 100-300 mm, with catches of fish up to 360 mm observed 

(Mallory and Metz, 1999). Because body size and foraging strategy of western grebes are 

similar to those of the merganser, staff assumed the same size range for grebe prey (USFWS, 

2004). 

Otter, bald eagle and osprey eat fish from multiple trophic level food groups. Methylmercury 

concentrations vary as a function of size and trophic level of prey. Therefore, different trophic 

levels of prey will have different acceptable concentrations of methylmercury. For these wildlife 

species, the total diet safe level (TDSL) can be described as: 

Equation 4.3: 

TDSL = (% diet TL2 * TL2conc) + (% diet TL3 * TL3conc) + (% diet TL4 * TL4conc) 

Where: % diet TL2 = percent of trophic level 2 biota in diet 

 % diet TL3 = percent of trophic level 3 biota in diet 

 % diet TL4 = percent of trophic level 4 biota in diet 

 TL2conc = concentration of methylmercury in TL2 biota 

 TL3conc = concentration of methylmercury in TL3 biota 

 TL4conc = concentration of methylmercury in TL4 biota 

In order to solve the above equation for the desired concentrations in TL2, TL3 and TL4 biota, 

concentrations in two trophic levels are put in terms of the concentration in the lowest trophic 

level. Equation 4.3 is then rearranged to solve for the lowest trophic level concentration. 

In order to express the concentration in a higher trophic level (i.e., TL4) in terms of TL2 

concentrations, staff used two types of translators: food chain multipliers (FCM) and trophic 

level ratios (TLR).16 FCM and TLR used in the calculation of Delta wildlife targets are shown in 

Table 4.4. Where possible, site-specific, existing fish concentration data was used to develop 

the ratios. A similar table of safe fish tissue concentrations to protect wildlife species using a 

national average bioaccumulation factor (BAF) between TL3 and TL4 of five is presented in 

Chapter 6 of Mercury Study Report to Congress Vol. 7 (USEPA, 1997b). Details regarding the 

calculation of the translators and their use were provided by the USFWS (2003 and 2004). 

 

16 A food chain multiplier (FCM) is the ratio of methylmercury concentrations in fish of different trophic levels. A FCM 

represents the biomagnification of mercury between 2 successive levels of the food chain. The FCM is determined 

using mercury concentration data in fish in a predator-prey relationship. Example: the FCM for trophic level 4 fish 

is the ratio of methylmercury in large TL4 fish to methylmercury in small TL3 fish. 

A trophic level ratio (TLR) is the ratio of methylmercury concentrations in fish of different trophic levels, but is 

derived using data for fish in the same size classification. For example, an osprey may consume sunfish (TL3) and 

bass (TL4). A 350 mm sunfish, though, is too large to be preyed upon by an equivalently-sized smallmouth bass. 

Therefore, the ratio of mercury concentration in TL4 to TL3 fish eaten by osprey is termed a TLR rather than a 

FCM. 

Delta Methylmercury TMDL Report 41 April 2010 
Table 4.4: Food Chain Multipliers and Trophic Level Ratios for Delta Wildlife Target Development 

Translator Value Source 

Relevant Wildlife 

Species (a)

Trophic Level Ratio (TLR) 

TLR 4/3 3.0 

Ratio between existing MeHg concentrations in large TL4 fish 

(150-350 mm length) and large TL3 fish (150-350 mm length). 

Calculated from Delta-wide average fish tissue levels; see 

Appendix B. 

Bald eagle, osprey 

Food Chain Multipliers (FCM) 

FCM 4/3 8.1 

Ratio between existing MeHg concentrations in large TL4 fish 

(150-350 mm length) and small TL3 fish (50-150 mm). 

Calculated from Delta-wide average fish tissue levels; see 

Appendix B. 

River otter 

FCM 3/2 5.7 

Ratio between MeHg concentrations in large TL3 fish and 

small TL2 fish. From USFWS (2004) based on national 

averages. 

Bald eagle, 

peregrine falcon 

FCM piscivorous 

birds (FCM PB) 12.5 Ratio between MeHg in piscivorous bird tissue and in small TL3 prey fish. From USFWS (2003). 

Bald eagle, 

peregrine falcon 

FCM omnivorous 

birds (FCM OB) 10 

Ratio between MeHg in omnivorous bird tissue and in small, 

TL2/3 prey fish and other aquatic organisms. From USFWS 

(2003). 

Bald eagle, 

peregrine falcon 

(a) Wildlife species for which the translator is used to determine safe tissue levels. 

4.5.3.1 River Otter Safe Tissue Levels 

To calculate the safe concentrations for otter, the safe concentrations in TL3 and TL4 fish need 

to be determined. In order to solve for these two variables using Equation 4.3, the TL4 fish 

concentration is expressed in terms of the TL3 fish concentration. River otters eat a wide range 

of prey sizes. Large fish in the otter diet likely prey on small fish that otter also eat. Therefore, 

the TL4 variable is expressed using the TL3 concentration and a food chain multiplier 

(FCM 4/3). From the Delta field data, staff determined that the methylmercury concentration in 

large TL4 fish is 8.1 times the concentration in small TL3 fish. Safe tissue levels in TL3 and TL4 

fish for otter are determined by: 

 TDSLotter = (% dietTL3 * TL3conc) + (% dietTL4 * TL4conc) 

Where: TL4conc = TL3conc * FCM 4/3 

 0.107 mg/kg = (0.80 * TL3conc) + (0.20 * 8.1*TL3conc) 

Solving for TL3conc: 

 TL3conc = 0.044 mg MeHg/kg fish 

 TL4conc = 0.044 mg/kg * 8.1 = 0.36 mg MeHg/kg fish 

This equation produces safe levels of 0.04 and 0.36 mg/kg in small TL3 and large TL4 fish, 

respectively, which are shown in Table 4.3. 

Delta Methylmercury TMDL Report 42 April 2010 
4.5.3.2 Osprey safe tissue levels 

Safe methylmercury tissue levels for osprey are calculated like those for river otter, with the 

exception of the trophic level translator. Trophic level 3 and 4 fish eaten by osprey tend to be of 

similar sizes. Because there is not a food chain relationship between similarly sized fish, the 

osprey values are calculated using a trophic level ratio (TLR 4/3). On average in the Delta, 

methylmercury levels in large TL4 fish are 3.0 times the levels in large TL3 fish. 

 TDSLosprey = (% dietTL3* TL3conc) + (% dietTL4* TL4conc) 

Where: TL4conc = TL3conc * TLR 4/3 

 0.105 mg/kg = (0.90* TL3conc) + (0.10* 3.0*TL3conc) 

Solving for TL3conc: 

 TL3conc = 0.088 mg MeHg/kg fish 

 TL4conc = 0.088 mg/kg * 3.0 = 0.26 mg MeHg/kg fish 

4.5.3.3 Bald Eagle Safe Tissue Levels 

Calculation of methylmercury tissue levels for bald eagle is slightly more complicated because 

bald eagles consume omnivorous birds (OB), piscivorous birds (PB), and fish. The omnivorous 

birds of concern in the bald eagle diet feed on trophic level 2 aquatic prey (mostly 

invertebrates). To solve the equation, safe tissue concentrations in the other eagle prey types 

are expressed in terms of the lowest food chain level (TL2) common to all prey types (USFWS, 

2004). To translate the TL2 concentration into the piscivorous bird safe level, staff used the 

food chain multiplier for TL3 small fish (FCM 3/2) and the food chain multiplier relating 

piscivorous birds and small TL3 fish (FCM PB). Like osprey, bald eagles tend to eat TL3 and 

TL4 fish of similar size, hence the use of the TL4/3 ratio. 

TDSLbald eagle = (% dietTL3* TL3conc) + (% dietTL4* TL4conc) + (%dietOB*OBconc) +(%dietPB*PBconc)

Where: TL3conc large fish = TL2conc * FCM 3/2 

 TL4conc large fish = TL2conc * FCM 3/2 * TL 4/3 

 OBconc = TL2conc * FCM OB

PBconc = TL2conc * FCM 3/2 * FCM PB

0.195 mg/kg = (0.58*5.7*TL2conc) + (0.13*5.7*3.0*TL2conc) + (0.13 *10*TL2conc) + 

(0.05* 5.7*12.5*TL2conc) 

Solving for TL2conc: 

 TL2conc = 0.019 mg MeHg/kg fish (not eaten by eagles; used to determine other safe levels)

 TL3conc large fish = 0.019 * 5.7 = 0.11 mg MeHg/kg fish 

 TL4conc large fish = 0.019 * 5.7 * 3.0 = 0.31 mg MeHg/kg fish 

 OBconc = 0.019 * 10 = 0.19 mg MeHg/kg omnivorous birds 

 PBconc = 0.019 * 5.7 * 12.5 = 1.35 mg MeHg/kg piscivorous birds 

Delta Methylmercury TMDL Report 43 April 2010 
4.5.3.4 Peregrine Falcon Safe Tissue Levels 

Peregrine falcons consume almost exclusively avian prey, some of which is aquatic-dependent. 

To solve for safe concentrations in omnivorous and piscivorous bird prey, these terms are 

expressed as functions of the lowest trophic level common to the birds’ food web, which is TL2 

aquatic prey (USFWS, 2004). 

 TDSLperegrine = (%dietOB*OBconc) + (%dietPB*PBconc) 

Where: OBconc = TL2conc * FCM OB 

 PBconc = TL2conc * FCM 3/2 * FCM PB 

 0.139 mg/kg = (0.10 * 10 * TL2conc) + (0.05 * 5.7* 12.5 * TL2conc) 

Solving for TL2conc: 

 TL2conc = 0.030 mg MeHg/kg fish (not eaten by peregrines; used to 

determine other safe levels)

 OBconc = 0.030 * 10 = 0.30 mg MeHg/kg omnivorous birds 

 PBconc = 0.030 * 5.7 * 12.5 = 2.2 mg MeHg/kg piscivorous birds 

Note that the safe fish tissue levels in Table 4.3 are partially watershed-dependent and are 

specific to the Delta. The acceptable, average fish tissue concentrations for wildlife consuming 

from one trophic level will be consistent across different water bodies. This is because all of the 

parameters used to calculate the safe fish levels (species body weight, consumption rate and 

reference dose) were obtained from published literature and apply on a national or regional 

scale (Table 4.2). For species consuming fish from two trophic level classifications or 

piscivorous birds, translators (FCM or TLR) were used to calculate the safe concentrations in 

prey fish and piscivorous birds. These translators should be derived from site-specific data 

when possible and may differ between watersheds. For the Delta targets, the TLR and FCM 

between trophic level 4 and 3 fish were specific to the Delta. The FCMs for piscivorous birds, 

omnivorous birds and trophic level 3 fish were literature-derived average values. 

Central Valley Water Board staff is not proposing safe tissue levels in piscivorous or omnivorous 

birds as TMDL targets. Data are lacking to compare safe levels in bird prey with existing 

conditions. By lowering methylmercury concentrations in fish and aquatic prey to safe levels 

shown in Table 4.3, staff anticipates that concentrations in birds feeding in the aquatic food web 

will decline to safe levels as well. In particular for peregrine falcon, the desired safe level in 

piscivorous birds is 2.2 mg/kg. Dividing the safe piscivorous bird level by 12.5 (FCM PB) results 

in a safe level in TL3 prey fish (150-350 mm length) of 0.17 mg/kg, which is above the proposed 

target for large TL3 fish. 

Wildlife targets for TL3 and TL4 fish greater than 150 mm in length may be directly compared 

with targets developed to protect human consumers, as discussed in the following section. In 

Section 4.7, the wildlife and human targets that are trophic level and size-specific are 

incorporated into a single target based on largemouth bass that is protective of humans and all 

wildlife species of concern. 

Delta Methylmercury TMDL Report 44 April 2010 
4.6 Human Health Targets 

Numeric targets can be developed to protect humans in a manner analogous to targets for 

wildlife. A reference dose, average body weight and consumption rates are used along with 

Equations 4.1 and 4.3 to calculate safe fish tissue levels. In this section, the human health 

exposure parameters are discussed. 

4.6.1 Acceptable Daily Intake Level 

Central Valley Water Board staff used the USEPA RfD for methylmercury (USEPA, 2001) in 

Delta target calculations. The lowest level of methylmercury exposure that caused harm was 

determined in tests of neuropsychological function in children in the Faroe Islands and other 

sites exposed to methylmercury in fish. The USEPA divided the lowest effect level by ten to 

calculate a final RfD of 0.1 μg methylmercury/kg bwt/day (USEPA, 2001). The USEPA 

describes its RfD an exposure level that is not expected to cause harm over a lifetime of 

exposure on a daily basis. The ten-fold uncertainty factor accounts for differences in the extent 

to which individuals absorb, metabolize, and react to methylmercury. The USEPA RfD is 

applied to the general population.17 

4.6.2 Body Weight & Consumption Rate 

This report uses the USEPA’s standard adult bodyweight of 70 kg. Using an average pregnant 

female bodyweight (65 or 67 kg) would have very little difference on the calculation of mercury 

targets in fish. 

Consumption rate is the most difficult of the fish tissue target variables to select because human 

consumption is variable. The amount of methylmercury ingested is highly dependent on the 

amount of fish and the sizes and species of fish consumed. The preferred level of Delta fish 

consumption is bounded by the limited amount recommended in the existing fish advisory and 

the rate of a very high consumer. People could eat unlimited quantities of Delta fish if the fish 

mercury concentration was zero. Human health is best protected by both cleanup and 

education. Education is needed until the effects of mercury reduction are seen in fish tissue 

levels. During the TMDL implementation period, consumers should be encouraged to eat 

smaller fish and species with lower mercury concentrations. 

A comprehensive survey of consumption of Delta fish has not been conducted. Thus, staff 

examined San Francisco Bay and national fish consumption studies, as well as several 

localized and pilot studies in the Delta, to develop Delta-specific consumption scenarios and 

ultimately recommend targets for human protection. 

 

17 “In the studies so far published on subtle neuropsychological effects in children, there has been no definitive 

separation of prenatal and postnatal exposure that would permit dose-response modeling. That is, there are 

currently no data that would support the derivation of a child (versus general population) RfD. This RfD is 

applicable to the lifetime daily exposure for all populations, including sensitive subgroups. It is not a developmental 

RfD per se, and its use is not restricted to pregnancy or developmental periods” Water Quality Criterion for 

Methylmercury, Section 4-6 (USEPA, 2001). 

Delta Methylmercury TMDL Report 45 April 2010 
The USEPA recommends default consumption rates for the general population and some 

subpopulations (USEPA, 2000a). Default consumption rates are derived from data collected 

nationwide as part of the 1994-96 USDA Continuing Survey of Food Intake by Individuals 

(CFSII). The USEPA reports rates separately for consumption of freshwater and marine fish. 

The USEPA recommends a fish intake rate of 17.5 g/day (about one 8-ounce uncooked fish 

meal every two weeks18) to protect the general population consuming freshwater and estuarine 

fish. This value represents the 90th percentile consumption rate for all survey participants, 

including those who do not eat fish. In selecting the 90th percentile, rather than the mean or 

median, the USEPA intended to recommend a consumption rate that is protective of the 

majority of the entire population. The USEPA recommended a consumption rate of 142.4 g/day 

(four to five 8-ounce, uncooked, portions per week) of local fish to represent anglers who use 

locally caught fish as a main source of protein. This value represents the 99th percentile 

consumption rate for all survey participants. 

A detailed survey of consumption by anglers in San Francisco Bay was conducted in 1998 and 

1999 (SFEI, 2000). The consumption rates for the 90th and 95th percentiles of anglers that were 

“consumers” (consumed Bay fish at least once prior to the interview) were 16 and 32 g/day, 

respectively. The San Francisco Bay Mercury TMDL selected the consumption rate for the 

95th percentile of anglers (32 g/day) for calculation of the San Francisco Bay fish mercury target 

(0.2 mg/kg) to protect people who choose to eat San Francisco Bay fish on a regular basis 

(Johnson and Looker, 2004; SFBRWQCB, 2006). 

California Department of Public Health staff interviewed members of communities thought to 

have high consumption rates (CDHS, 2004) and conducted several pilot fish consumption 

surveys in the Delta (CDHS, 2005 and 2006; Ujihara, 2006). From the interviews, CDPH 

learned that being able to safely eat Delta fish is important to many people. Members of all 

races and many ethnic groups fish in the Delta. Preferences for angling location, language 

spoken, and fish species are important for developing education and outreach programs. 

The CDPH conducted small surveys of anglers in three parts of the Delta (CDHS, 2005 and 

2006; Ujihara, 2006). Of boaters docking in Contra Costa County surveyed in 2005, 50% 

reported never eating Delta fish; 3% ate it more than once per week. Of boat and shore anglers 

on the Sacramento River between Rio Vista and the American River interviewed during salmon 

season in 2003, 17% ate Delta fish more than once per week. Shore anglers at two southern 

Delta and two San Joaquin River sites outside the Delta were interviewed in October/November 

2005. Of the total respondents who ate any fish in the 30-day period prior to the survey, the 

geometric mean consumption rates were 22, 17, and 27 grams uncooked fish per day for locally 

caught, commercial, and total fish, respectively; these rates are less than one 8-ounce meal per 

week. Anglers were typically male. Many respondents in the Sacramento River and Delta/San 

Joaquin River angler surveys said that women and children in their households eat Delta fish. 

 

18 Although the target calculations use bodyweights and consumption rates for adult humans, the resulting fish tissue 

levels protect children as well. Children’s bodyweights and smaller portion sizes can also be fitted into 

Equations 4.1 and 4.3. The OEHHA has published a table of sizes of typical meals of fish that correspond to 

smaller bodyweights (OEHHA, 1999). Children would only be at risk of mercury toxicity if they consumed more 

than the average portion for their body size. 

Delta Methylmercury TMDL Report 46 April 2010 
A recent fish consumption and advisory awareness survey of low-income women at a WIC19

clinic in Stockton found that 32% of the 500 survey participants ate Delta fish and 95% ate 

commercial fish (Silver et al., 2007). For participants who ate any fish in the 30-day period prior 

to the survey, the geometric mean consumption rates equaled 13, 33, and 35 grams uncooked 

fish per day for Delta, commercial, and total fish, respectively.20 Cambodian, Asian/Pacific 

Islander, and African American participants had the highest mean consumption rates (24, 22, 

and 18 grams uncooked fish per day, respectively). 

In 2005-2008, researchers from University of California Davis interviewed anglers and 

community members in the Delta about eating fish (Shilling, 2009). The study area included the 

Sacramento River between Rio Vista and the American River and the Sacramento Deep Water 

Ship Channel. The average and 95th percentile rates of consumption of locally caught fish were 

11 and 52 g/day uncooked fish/day, respectively. Women and men ate fish at similar rates. 

Average consumption rates of locally caught fish were highest for Lao, African American, and 

Vietnamese participants. 

4.6.3 Consumption of Fish from Various Trophic Levels & Sources 

Species and size of fish as well as consumption rate affect methylmercury intake. It is difficult 

to estimate amounts of various species of sport fish that might be consumed from the Delta. 

Based on the CSFII national survey, the USEPA assumed that humans eat freshwater and 

estuarine fish from trophic levels two (3.8 g/day), three (8.0 g/day) and four (5.7 g/day) (USEPA, 

2001). These rates are 21.7, 45.7, and 32.6% of the total 17.5 g/day, respectively. Trophic 

level 2 species, such as clams, crayfish, shrimp and shimofuri goby, are harvested from the 

Delta for human consumption (Appendix C). However, CDFG creel surveys (CDFG, 2000-

2001) and anecdotal information provided by CDFG staff (Schroyer, 2003) indicate that many 

Delta anglers do not take home TL2 species. As described in Figure C.1 in Appendix C, the 

creel surveys indicate that Delta anglers may target an almost even mix of TL3 (American shad, 

salmon, sunfish, splittail) and TL4 (catfish and striped bass) fish in the Sacramento and 

Mokelumne Rivers subareas of the Delta, and primarily TL4 species (striped bass and catfish) 

throughout the rest of the Delta. Anecdotal information provided by CDFG staff (Schroyer, 

2003) indicates that even in the rest of the Delta, many anglers take home a mix of TL3 and TL4 

fish species. In the Delta consumption surveys described in previous paragraphs, anglers 

reported taking home catfish, striped bass, carp, bluegill, salmon, largemouth bass, crappie, 

sturgeon, and crayfish (CDHS, 2005 and 2006; Ujihara, 2006). 

When evaluating potential fish tissue targets, staff considered five different tropic level 

distributions of locally caught fish (Table 4.5). Staff considered the TL2/3/4 mixture used by the 

USEPA for one distribution and Delta-specific information to develop four other distributions: 

100% TL4, even mix of TL3 and 4, and an even mix of TL3 and 4 with small amounts of TL2 

species (e.g., clams and shrimp). 

 

19 Special Supplemental Nutrition program for Women, Infants, and Children (WIC). 20 This study reported consumption in grams of cooked fish. In order to compare the studies, Central Valley Water 

Board staff converted units of cooked fish to uncooked fish by multiplying by 1.25. 

Delta Methylmercury TMDL Report 47 April 2010 
When determining safe levels of Delta fish consumption, staff also considered the intake of 

methylmercury from commercial fish (see definition of RSC in Section 4.4). Many fish 

consumers eat a combination of locally caught and commercially bought fish. Based on the 

national CFSII survey, the USEPA assumes an average consumption rate of commercial fish of 

12.46 g/day, which results in an average daily intake of 0.027 μg methylmercury/kg bwt-day 

(USEPA, 2001). For people eating fish from commercial markets and the Delta, the safe intake 

level of methylmercury from Delta fish is the reference dose minus the methylmercury from 

commercial fish (0.1 μg/kg-day minus 0.027 μg/kg-day equals 0.073 μg/kg-day).21 

4.6.4 Safe Rates of Consumption of Delta Fish 

The USEPA issued a recommended criterion of 0.3 mg/kg methylmercury in locally caught fish 

consumed by humans (USEPA, 2001) 22. The USEPA human health criterion was calculated 

using a default consumption rate of freshwater/estuarine fish of 17.5 g/day (about one meal 

every two weeks) and commercial (marine) fish of 12.46 g/day. The criterion assumed that 

humans eat freshwater and estuarine fish from TL2 (21.7%), TL3 (45.7%) and TL4 (32.6%). 

However, the USEPA’s Water Quality Criterion report noted that the criterion can be adjusted on 

a site-specific basis to reflect regional or local consumption patterns and/or specific populations 

of concern. These include the consumption rates of local fish and the RSC estimate. For 

example, the San Francisco Bay mercury fish tissue objective of 0.2 mg/kg was calculated using 

a consumption rate of 32 g/day (about one meal per week) derived from a San Francisco Bay 

consumption survey. The San Francisco Bay objective is applied to the average mercury 

concentration in the five most commonly consumed Bay fish species: striped bass, California 

halibut, jacksmelt, white sturgeon, and white croaker (three TL4 species and two TL3 fish 

species; SFBRWQCB, 2006). 

In the absence of Delta-specific consumption rates, the USEPA default consumption rate 

(17.5 g/day), San Francisco Bay consumption rate (32 g/day), and USEPA recommended 

consumption rate for anglers whose main source of protein is from locally caught fish 

(142.4 g/day) were used in Equation 4.1 to estimate the safe methylmercury level in the total 

diet for humans consuming Delta fish (Table 4.5). In addition, scenarios were developed for 

anglers who consume Delta and commercial fish, and for anglers who consume only Delta fish. 

For each of the total diet safe levels associated with the different consumption rates, different 

distributions of locally caught fish were considered. Because some Delta consumers eat TL2 

species, two scenarios assume Delta consumers eat small proportions of TL2 species. 

Equation 4.3 was used to develop safe levels for each trophic level of Delta fish. In order to 

solve Equation 4.3 for the desired concentrations in TL2, TL3 and TL4 biota, concentrations in 

the higher trophic levels are put in terms of the concentration in the lowest trophic level. 

 

21 Most commercial fish do not come from the Delta. The most popular fish and seafood bought in commercial 

markets are marine species such as scallops, shrimp, and tuna. The average consumption rate of marine fish 

reported by all respondents in the national CFSII survey was 12.46 g/day (three meals every two months; USEPA, 

2001). The average concentration of methylmercury in commercial species weighted by frequency of consumption 

is 0.16 mg/kg (USEPA, 2001) 22 The USEPA rounded from 0.288 mg/kg to 0.3 mg/kg for use as its recommended methylmercury criterion. Central 

Valley Water Board staff’s calculations throughout the rest of this report are rounded to two decimal places, e.g., 

0.29 mg/kg. 

Delta Methylmercury TMDL Report 48 April 2010 
Equation 4.3 is then rearranged to solve for the lowest trophic level concentration. In order to 

express the concentration in a higher trophic level, trophic level ratios were used. The TLRs 

used in the calculation of Delta human targets are shown in Table 4.6. Existing Delta fish 

concentration data were used to develop the ratios. The following example illustrates how the 

trophic level fish targets were developed for Scenario A.1 in Table 4.5 using Equations 4.1 

and 4.3. 

Per Equation 4.1: 

 Safe MeHg in total diet = (Human RfD - Relative source contribution) * Body weight

 of Delta fish Consumption rate 

 0.29 mg/kg = 0.073 μg MeHg/kg-day * 70 kg 

 17.5 g/day 

Per Equation 4.3: 

 0.29 mg/kg = (% dietTL2* TL3conc) + (% dietTL3* TL3conc) + (% dietTL4* TL4conc) 

Where: TL3conc = TL2conc * TLR 3/2 

 TL4conc = TL2conc * TLR 3/2 * TLR 4/3 

 0.29 mg/kg = (21% * TL2conc) + (46% * TL2conc * 4.5) + (33% * TL2conc * 4.5 * 2.9) 

Solving for TL2conc: 

 TL2conc = 0.30 / (0.21 + (0.45*4.5) +(0.33*4.5*2.9)) = 0.046 mg/kg in shrimp & clams 

 TL3conc = 0.046 mg/kg * 4.5 = 0.20 mg/kg in 150-500 mm fish 

 TL4conc = 0.046 mg/kg * 4.5 * 2.9 = 0.45 mg/kg in 150-500 mm fish 

The highlighted safe levels for TL3 and TL4 fish in Scenarios A.1, A.4, B.4 and E.3 are 

evaluated as fish tissue objective alternatives in Chapter 3 of the draft Basin Plan Amendment 

staff report. As indicated by Table 4.5, potential safe levels of mercury in large Delta TL4 fish 

range from 0.05 to 0.80 mg/kg. Safe methylmercury concentrations can be higher when 

consumers of Delta fish do not eat commercial fish. However, in interviews of local community 

based groups and pilot surveys, most respondents who eat Delta fish consume commercial fish 

as well (CDHS, 2004; Silver 2007; and Ujihara, 2006). Staff therefore narrowed the options for 

further consideration by assuming Delta fish consumers eat commercial fish unless consumers 

are highly dependent on Delta fish (Scenario E). 

Including small amounts of TL2 species into the diet distribution (Scenarios A.2, A.3, B.2, 

and B.3) makes little difference in the safe methylmercury concentrations in TL3 and TL4 fish, 

relative to an even mix of just TL3 and TL4 fish. To protect the many Delta anglers who likely 

do not eat TL2 species, staff proceeded with consideration of TL3 and 4 fish only. 

To further assess the feasibility of attaining the targets, staff compared them to regional 

background conditions defined by a recent study by the USEPA and Oregon State University 

(Peterson et al., 2007). This study included the collection and analysis of 2,707 large TL3 and 

TL4 fish from 626 streams and river segments in the western United States, including California, 

using a probability design. The purpose of the study was to assess the distribution of mercury 

Delta Methylmercury TMDL Report 49 April 2010 
in fish across the western United States. Central Valley Water Board staff evaluated the study 

results in terms of the existing fish mercury levels in the Delta and alternative fish tissue targets 

(Foe, 2007). 

Only about 1 to 3% of the waterways evaluated by the regional study had fish mercury 

concentrations higher than those observed in the Mokelumne/Cosumnes subarea of the Delta. 

Likewise, fish mercury concentrations in the Sacramento, San Joaquin, and Yolo Bypass 

subareas were in the top 20 to 25% of fish mercury concentrations observed throughout the 

western United States. This confirms that Delta fish have elevated concentrations in 

comparison to regional background levels and suggests that the Delta and its tributary 

watersheds contain mercury sources in addition to atmospheric deposition, e.g., abandoned 

mines and sites where the mercury is efficiently converted to methylmercury that 

bioaccumulates in the aquatic food web (Foe, 2007). Of the sampled waterways in the western 

United States, none supported a fish population with mercury concentrations as low as 

Scenario E.3 (0.05 mg/kg in large TL4 fish) (Peterson et al., 2007; Foe, 2007). Therefore, this 

target may not be attainable. In contrast, about 30% to 40% of the sampled waterways 

supported a fish population with mercury concentrations lower than Scenarios A.1, A.4, and B.4, 

suggesting that these scenarios may be attainable with implementation of a vigorous control 

program. 

As discussed in the draft Basin Plan Amendment staff report, the TL3 and TL4 targets produced 

by Scenario B.4 of 0.08 mg/kg and 0.24 mg/kg, respectively, are recommended by Central 

Valley Water Board staff for the protection of humans for several reasons: 

• They fully protect wildlife species consume large fish, including threatened and 

endangered species as required by the Endangered Species Act. 

• They reasonably protect people who eat Delta fish by safely allowing the consumption of 

one eight-ounce meal per week of Delta fish, a consumption rate greater than the USEPA 

default rate used in Scenarios A and C. These objectives are therefore more protective 

of people who by custom, need, or enjoyment, more frequently eat Delta fish. 

• They incorporate local consumption patterns, which show that Delta anglers commonly 

target fish like salmon (TL3) and striped bass (TL4). 

• They are consistent with the fish tissue objectives approved by the State Water Board for 

San Francisco Bay (SFBRWQCB, 2006; SWRCB, 2007). Like the Scenario B.4 targets, 

the methylmercury objective recommended for the Bay is based on protecting people 

who eat 32 g/day of local fish. Scenario B.4 takes into consideration that people, fisheating wildlife and their prey (e.g., anadromous species) travel between the Delta and 

San Francisco Bay. 

• They are attainable because they are not less than background fish mercury levels in the 

western United States and they can be reliably measured (given current analytical 

methods for water and fish; see Section 5.2 in Chapter 5). 

These targets are carried forward throughout the rest of this report for use in the food web 

evaluation, linkage analysis and development of methylmercury source allocations. 

Delta Methylmercury TMDL Report 50 April 2010 
Table 4.5: Safe Concentrations of Methylmercury in Delta Fish by Trophic Level (TL) to Protect Humans 

Calculated Using Varying Assumptions about Consumption Rates and Trophic Level 

Distribution. 

Distribution of 

Locally Caught Fish 

by TL 

Safe Concentration of 

MeHg in Fish by TL 

(mg/kg) (d)

Scenario 

Body 

Weight 

(kg) 

Acceptable 

Daily Delta 

Fish MeHg 

Intake Level 

(μg/kg-day) (a)

Total 

Consumption 

Rate of Delta Fish

(g/day) (b)

Safe MeHg

Level in Total

Diet of 

Delta Fish 

(mg/kg) (c) TL2 TL3 TL4 TL2 TL3 TL4 

For people eating commercial and Delta fish: 

A.1 21.7% 45.7% 32.6% 0.04 0.20 0.58 

A.2 10% 45% 45% 0.04 0.16 0.47 

A.3 5.0% 47.5% 47.5% 0.03 0.16 0.45 

A.4 --- 50% 50% 0.15 0.43 

A.5 

70 0.073 17.5 0.29 

--- --- 100% 0.29 

B.1 21.7% 45.7% 32.6% 0.02 0.11 0.32 

B.2 10% 45% 45% 0.02 0.09 0.26 

B.3 5.0% 47.5% 47.5% 0.02 0.09 0.25 

B.4 --- 50% 50% 0.08 0.24 

B.5 

70 0.073 32 0.16 

--- --- 100% 0.16 

For people eating only Delta fish:

C.1 21.7% 45.7% 32.6% 0.06 0.28 0.80 

C.2 --- 50% 50% 0.21 0.59 

C.3 

70 0.1 17.5 0.40 

--- --- 100% 0.40 

D.1 21.7% 45.7% 32.6% 0.03 0.15 0.44 

D.2 --- 50% 50% 0.11 0.33 

D.3 

70 0.1 32 0.22 

--- --- 100% 0.22 

E.1 21.7% 45.7% 32.6% 0.01 0.03 0.10 

E.2 --- 50% 50% 0.03 0.07 

E.3 

70 0.1 142.4 0.05 

--- --- 100% 0.05 

(a) For people eating fish from commercial markets and the Delta, the safe intake level of methylmercury from Delta fish is the

USEPA reference dose minus the methylmercury from commercial fish (0.1 μg/kg-day minus 0.027 μg/kg-day = 0.073 μg/kgday). Scenarios C through E assume no commercial fish are consumed. 

(b) The USEPA human health criterion was calculated using a default consumption rate of freshwater/estuarine fish of 17.5 g/day

and of commercial (marine) fish of 12.46 g/day, as derived from national dietary surveys (USEPA, 2001). The criterion 

assumed that humans eat freshwater and estuarine fish from TL2 (21.7%), TL3 (45.7%) and TL4 (32.6%). 

(c) The USEPA criterion calculations yielded a methylmercury value of 0.288 mg methylmercury/kg fish, which the USEPA rounded 

to one significant digit. The Region 2 San Francisco Bay Mercury TMDL target calculations yielded a methylmercury value of 

0.16 mg methylmercury/kg fish, which Region 2 also rounded to one significant digit in the San Francisco Bay Mercury TMDL 

report (Johnson and Looker, 2004). 

(d) Values were calculated using Equation 4.3 and trophic level ratios presented in Table 4.6. Values were rounded to two decimal 

places. The highlighted targets (Scenarios A.1, A.4, B.4 and E.3) are evaluated as fish tissue objective alternatives in the draft 

Basin Plan Amendment staff report. The TL3 and TL4 targets produced by Scenario B.4 are recommended for the protection of 

humans that consume fish from throughout the Delta and are carried forward throughout the rest of this report for use in the 

linkage analysis and development of allocations. 

Delta Methylmercury TMDL Report 51 April 2010 
Table 4.6: Trophic Level Ratios for Delta Human Target Development 

Translator Value Source 

TLR 4/3 2.9 

Ratio between existing MeHg concentrations in large TL4 fish (150 mm [or legal catch 

limit] to 500 mm length) and large TL3 fish (150 mm [or legal catch limit] to 500 mm 

length). Calculated from Delta-wide average fish tissue levels; see Appendix B. 

TLR 3/2 4.5 

Ratio between existing MeHg concentrations in large TL3 fish (150-500 mm length) and 

TL2 species potentially consumed by humans (shrimp and clams). Calculated from 

Delta-wide average fish tissue levels; see Appendices B, C and K. 

4.7 Trophic Level Food Group Evaluation 

As noted in the previous section, Central Valley Water Board staff recommends targets of 

0.08 and 0.24 mg/kg in large TL3 and TL4 fish, respectively, for the protection of humans that 

consume fish from throughout the Delta. In this section, the relationships between 

methylmercury concentrations in large TL4 fish and the other trophic level food groups are 

examined. The purpose of this analysis is to determine whether consistent relationships might 

exist between the assemblages of fish and, if so, whether it might be possible to describe safe 

mercury ingestion rates for humans and wildlife species in terms of large TL4 fish. This analysis 

enables staff to determine whether a water quality objective based on methylmercury in large 

fish developed for the protection of humans may or may not be protective of wildlife species that 

consume smaller or lower trophic level fish. 

4.7.1 Data Used in Trophic Level Food Group Evaluation 

Mercury concentrations for each trophic level food group sampled in the Delta are presented in 

Appendix K and summarized in Table 4.7. Values presented are average concentrations, 

weighted by the number of individual fish in composite samples. The trophic level food group 

concentrations are the result of analyzing 1,048 composite samples of 4,578 fish from 

23 species in the Delta (Table B.2 and B.3 in Appendix B and Appendix K). Figure 4.1 

illustrates the fish sampling locations used in the trophic level food group evaluation. The 

sampling was conducted by CDFG, SFEI, University of California, Davis, the Toxic Substances 

Monitoring Program, and the Sacramento River Watershed Program (Davis et al., 2000; 

Davis et al., 2003; Slotton et al., 2003; LWA, 2003; SWRCB-DWQ, 2002). 

The data for each food group were assembled after considering four general rules. First, the 

data were restricted to samples collected between 1998 and 2001, the period with the most 

comprehensive sampling across the Delta. Second, migratory species (salmon, American shad, 

steelhead, sturgeon, and striped bass) were excluded. These species likely do not reside yearround at the locations in the Delta where they were caught and their tissue mercury levels may 

not show a positive relationship with the mercury levels in resident animals. In addition, data for 

migratory species are not available for all Delta subareas, precluding an analysis to determine 

whether such a relationship might exist. A review of data available for several 

Delta Methylmercury TMDL Report 52 April 2010 
commercial species (striped bass, salmon, blackfish and crayfish) is provided in Appendix C.23 

Third, fish samples with lengths greater than 500 mm were not included. Data for fish larger 

than 500 mm are available for only some subareas. Capping the size at 500 mm allows 

comparable data for all Delta subareas. Finally, only fish fillet data were used in the human and 

eagle trophic level food group analysis. Humans typically consume fish fillets, while wildlife 

species, including eagles, eat whole fish. However, all the data for large fish typically 

consumed by eagles and other large wildlife species are from fillet samples, making it 

necessary to use fillet information for these species.24 Whole fish data were used for the 

smaller wildlife species food groups. 

Of the eight Delta subareas identified in Section 2.2.2 and Figure 2.2, three of the subareas 

were not included in the trophic level food group evaluation due to inadequate information. No 

fish were sampled from the Marsh Creek subarea between 1998 and 2001. In addition, small 

fish were sampled throughout the Yolo Bypass-South subarea between 1998 and 2001, but 

large fish were sampled only in the southernmost area; hence, the mercury levels in the trophic 

level food groups are not geospatially comparable. The only fish sampling conducted in the 

Yolo Bypass-North subarea took place in Greens Lake, which is not considered representative 

of the entire subarea. In addition, only large TL4 fish were sampled; no small fish were 

sampled. 

Table 4.8 provides a comparison of the average mercury concentrations for each trophic level 

food group sampled in the Delta (Table 4.7) to the recommended targets for the species with 

the lowest safe fish methylmercury levels within each trophic level food group. The comparison 

indicates that the recommended targets for wildlife protection are already met in the Central and 

West Delta subareas. In addition, the comparison indicates that greater reductions may be 

required to achieve the recommended target for large TL4 fish developed for human protection 

than for the recommended targets for smaller and lower trophic level fish developed for wildlife 

protection. The following section describes a more direct method for comparing the level of 

protection provided by the different trophic level food group targets. 

4.7.2 Trophic Level Food Group Comparisons 

Regressions between methylmercury concentrations in large TL4 fish and the other TL food 

groups are presented in Figure 4.2. The relationships were evaluated using linear, exponential, 

logarithmic, and power curves; in each case the type of curve that provided the highest R2

 value 

was selected. All of the correlations were statistically significant (P<0.05 or less). The 

regressions demonstrate that there are predictable relationships between mercury 

concentrations in large TL4 fish and the other trophic level food groups in the Delta. 

 

23 Methylmercury concentrations in salmon and striped bass are important to human risk assessment because people 

frequently attempt to catch these two species. Average mercury concentrations in striped bass are similar to 

mercury levels in largemouth bass. The available mercury data for salmon indicate that their tissue concentrations 

are much lower that the mercury levels in bass (0.04 to 0.12 mg/kg). See Appendix C for more information about 

striped bass and salmon. 24 Researchers in New York found that concentrations in whole body and muscle of large TL3 and TL4 fish were not 

significantly different (Becker and Bigham, 1995), suggesting that it is appropriate to use fillet data to evaluate 

exposure to wildlife species. 

Delta Methylmercury TMDL Report 53 April 2010 
Table 4.9 presents the predicted safe dietary mercury concentrations for each target species in 

terms of large TL4 fish calculated from the regression equations in Figure 4.2. The 

recommended target of 0.24 mg/kg in large TL4 fish developed for the protection of humans is 

lower than the corresponding safe large TL4 fish mercury concentrations predicted for the other 

TL food groups, which ranged from 0.30 mg/kg for Western grebe to 1.12 mg/kg for Western 

snowy plover. This indicates that the recommended targets for large TL3 and TL4 fish 

developed for protection of humans are most likely protective of wildlife species that consume 

smaller or lower trophic level fish. In other words, reductions in methylmercury levels needed to 

achieve the recommended targets for large TL3 and TL4 fish are expected to produce 

reductions in smaller fish sufficient to fully protect wildlife species. To ensure that wildlife 

species dining only on small fish are protected, staff proposes an additional target of 0.03 mg/kg 

methylmercury in TL2 and 3 fish less than 50 mm in length. This target represents the safe 

level for prey consumed by the California least tern, a piscivorous species listed by the federal 

government as endangered. As shown in Table 4.9, such a target for small fish also would 

protect the Western snowy plover. 

Table 4.7: Mercury Concentrations in Trophic Level Food Groups Sampled in the Delta 

Hg Concentrations (mg/kg) by Delta Subarea (a)

Trophic Level 

Food Group 

Central 

Delta 

Mokelumne 

River 

Sacramento 

River 

San Joaquin 

River 

West 

Delta 

TL4 Fish (150-500 mm) 0.26 0.92 0.56 0.50 0.32 

TL3 Fish (150-500 mm) 0.08 0.28 0.21 0.11 0.11 

TL4 Fish (150-350 mm) 0.20 0.75 0.46 0.42 0.24 

TL3 Fish (150-350 mm) 0.08 0.29 0.17 0.12 0.08 

TL3 Fish (50-150 mm) 0.03 0.09 0.04 0.04 0.03 

TL3 Fish (<50 mm) 0.02 0.07 0.03 0.04 0.03 

(a) The trophic level food group mercury levels are weighted averages of mercury levels for resident fish within each food 

group collected in each Delta subarea between 1998 and 2001. These food groups correspond to the proposed 

numeric targets developed earlier in Chapter 4. Weighted average mercury concentration is based on the number of 

fish in the composite samples analyzed, rather than the number of samples. 

Table 4.8: Percent Reductions in Fish Methylmercury Levels Needed to Meet Numeric Targets 

Delta Subareas 

Trophic Level 

Food Group 

Target 

Species (a) Target

(mg/kg)

Central

Delta 

Mokelumne 

River 

Sacramento 

River 

San Joaquin 

River 

West

Delta

TL4 Fish (150-500 mm) Human 0.24 8% 74% 57% 52% 25% 

TL3 Fish (150-500 mm) Human 0.08 0% 71% 62% 27% 27% 

TL4 Fish (150-350 mm) Osprey 0.26 0% 65% 43% 38% 0% 

TL3 Fish (150-350 mm) Grebe 0.08 0% 72% 53% 33% 0% 

TL3 Fish (50-150 mm) Kingfisher 0.05 0% 44% 0% 0% 0% 

TL3 Fish (<50 mm) Least Tern 0.03 0% 57% 0% 25% 0% 

(a) Only the recommended targets for the wildlife species with the lowest safe methylmercury concentrations in fish diet 

(Table 4.3) within each trophic level food group are evaluated. The proposed large TL3 and TL4 fish targets for human 

protection are lower than the targets proposed for protection of eagles. 

Delta Methylmercury TMDL Report 54 April 2010 
Table 4.9: Predicted Safe Concentrations of Methylmercury in 150-500 mm TL4 Fish 

and Standard 350-mm Largemouth Bass Corresponding to Trophic Level 

Food Group (TLFG) Targets for the Protection of Piscivorous Species.

Trophic Level Food Group / 

Species 

TLFG Target

(mg/kg) (a)

Predicted 

150-500 mm TL4 Fish 

Safe Level 

(mg/kg)

Predicted 

Standard 350-mm 

Largemouth Bass 

Safe Level

(mg/kg) (b)

TL4 Fish (150-500 mm) 

Human 0.24 (c) 0.28 

Bald eagle 0.31 (c) 0.36 

TL3 Fish (150-500 mm) 

Human 0.08 0.24 0.24 

Bald eagle 0.11 0.37 0.43 

TL4 Fish (150-350 mm) 

Osprey 0.26 0.33 0.36 

River otter 0.36 0.45 0.57 

TL3 Fish (150-350 mm) 

Western grebe 0.08 0.30 0.31 

Common merganser 0.09 0.35 0.38 

Osprey 0.09 0.35 0.38 

TL3 Fish (50-150 mm) 

Kingfisher 0.05 0.62 0.73 

Mink 0.08 0.90 1.06 

River otter 0.04 0.50 0.57 

Double-crested cormorant 0.09 0.96 1.15 

TL3 (<50 mm) 

California least tern 0.03 0.38 0.42 

Western snowy plover 0.10 1.12 1.34 

(a) The TLFG targets developed for bald eagle, osprey and river otter were developed using site-specific TLRs 

and/or FCMs combined with information provided in published literature. All other TLFG targets were 

entirely developed using information provided in published literature. 

(b) The calculation and purpose of the standard 350-mm largemouth bass mercury concentrations are 

described in the following section (Section 4.8). 

(c) The TL4 Goals are same as the TLFG Targets for human and eagle protection. 

Delta Methylmercury TMDL Report 55 April 2010 
Figure 4.1: Fish and Water Sampling Locations Included in the Trophic Level Food Group and 

Largemouth Bass Evaluations.

Delta Methylmercury TMDL Report 56 April 2010 
Figure 4.2: Comparison of Methylmercury Concentrations in Large (150-500 mm) TL4 Fish 

 and Other Trophic Level (TL) Food Groups. The regressions are used to predict 

safe diets for target species listed in Table 4.9 in terms of large TL4 fish. 

150-500 mm TL3 Fish vs.

150-500 TL4 Fish

y = 2.9204x + 0.0469

R2 = 0.8956

0.0

0.3

0.6

0.9

1.2

0.0 0.1 0.2 0.3 0.4

150-500 mm TL3

Fish Hg (mg/kg)

150-500 mm TL4 

Fish Hg (mg/kg)

0.24 0.08

150-350 mm TL4 Fish vs.

150-500 TL4 Fish

y = 1.1829x + 0.0231

R2 = 0.999

0.0

0.3

0.6

0.9

1.2

0.0 0.2 0.4 0.6 0.8 1.0

150-350 mm TL4

Fish Hg (mg/kg)

150-500 mm TL4 

Fish Hg (mg/kg)

0.33

0.26

150-350 mm TL3 Fish vs.

150-500 TL4 Fish

y = 0.4521Ln(x) + 1.438

R2 = 0.9695

0.0

0.3

0.6

0.9

1.2

0.0 0.1 0.2 0.3

150-350 mm TL3

Fish Hg (mg/kg)

150-500 mm TL4 

Fish Hg (mg/kg)

0.30

0.08

50-150 mm TL3 Fish vs. 

150-500 TL4 Fish

y = 0.5771Ln(x) + 2.3538

R2 = 0.9679

0.0

0.3

0.6

0.9

1.2

0.00 0.03 0.06 0.09

50-150 mm TL3 

Fish Hg (mg/kg)

150-500 mm TL4 

Fish Hg (mg/kg)

0.62

0.05

<50 mm TL3 Fish vs.

150-500 TL4 Fish

y = 0.6153Ln(x) + 2.5336

R2 = 0.8791

0.0

0.3

0.6

0.9

1.2

0.00 0.02 0.04 0.06 0.08

<50 mm TL3 

Fish Hg (mg/kg)

150-500 mm TL4 

Fish Hg (mg/kg)

0.38

0.03

Delta Methylmercury TMDL Report 57 April 2010 
4.8 Largemouth Bass Evaluation 

A goal of the TMDL is to link target methylmercury concentrations in fish to methylmercury 

concentrations in water to develop a goal for aqueous methylmercury that could then be used in 

development of an implementation plan. Chapter 5 (Linkage Analysis) describes the 

relationships between methylmercury in water and in largemouth bass in the Delta. Largemouth 

bass were selected for the linkage analysis for several reasons. Largemouth bass are a good 

bioindicator species. In addition, only largemouth bass data are available for the same 

sampling period and locations as the methylmercury water data (Figure 4.1). Largemouth bass, 

however, constitute only a portion of the diet of some of the human and wildlife consumers of 

Delta fish. The methylmercury targets determined above assume that humans and wildlife 

species consume a variety of sizes and species of fish from the Delta. In this section, the 

relationships between methylmercury concentrations in largemouth bass and the trophic level 

food groups were examined so that an implementation goal could be developed in terms of 

largemouth bass and, ultimately, linked to aqueous methylmercury. 

Most of the information on mercury concentrations in the various trophic level food groups in the 

Delta was collected as species-specific composite samples between 1998 and 2001. 

Therefore, the largemouth bass evaluation was conducted in four parts. First, the 

methylmercury concentrations in largemouth bass of a standard size were estimated for each 

Delta subarea using the relationships between length and methylmercury tissue concentration25

in samples collected in 2000. Second, correlations were run between standard 350-mm 

largemouth bass collected in 2000 and average concentrations of 300-400 mm largemouth bass 

(composite and individual samples) collected between 1998 and 2000. The year 2000 is 

significant because (1) aqueous methylmercury sampling began in March 2000 and (2) 

largemouth bass sampling adequate for the length/concentration regressions took place only in 

September/October 2000. The monthly March-October 2000 subset of the aqueous data has 

the greatest overlap with the lifespan of the largemouth bass sampled in September/October 

2000. As these correlations were highly significant, the third step was to examine correlations 

between mercury concentrations in standard 350-mm largemouth bass and composites of all 

trophic level food groups collected in the Delta between 1998 and 2001. The purpose of this 

analysis was to determine whether consistent relationships might exist between the different 

assemblages of fish and, if so, whether it might be possible to describe safe mercury ingestion 

rates for humans and wildlife species in terms of the methylmercury concentration in a standard 

350-mm largemouth bass. The final step was to determine a safe methylmercury concentration 

for each species in terms of the methylmercury concentration in 350-mm largemouth bass 

(Table 4.9). 

 

25 Determining the methylmercury concentration in a specific or “standard” size fish is a typical method of data 

analysis that allows comparison between sites and years. For largemouth bass from one site or subarea, mercury 

concentration is well correlated with length (Davis et al., 2003; data in Figure 4.3 in this report). This correlation is 

also useful in monitoring, as concentrations in fish in a range of lengths can be used to predict the concentration in 

a standard size. Hereafter, the mercury concentration in a “standard 350 mm largemouth bass” refers to the 

concentration obtained through a regression analysis as in Figure 4.3. 

Delta Methylmercury TMDL Report 58 April 2010 
4.8.1 Largemouth Bass Standardization 

The methylmercury content of a standard 350-mm length largemouth bass was determined at 

all sites where both water and fish tissue data were available (Figure 4.1) by regressing fish 

length against mercury body burden (Figure 4.3). Appendix K provides the concentration and 

length data for largemouth bass sampled in the Delta. Table 4.10 presents the predicted 

mercury values for 350 mm bass at each location where both water and fish tissue data were 

available. The predicted mercury concentration in standard 350 mm largemouth bass varied by 

a factor of five across the Delta (0.19 mg/kg in the Central Delta to 1.04 mg/kg in the 

Mokelumne River). Mercury concentration in a standard length 350 mm largemouth bass was 

selected because the length is near the middle of the size range collected at each site and 

therefore maximizes the predictive capability of the regression (Davis et al., 2003). Three 

hundred and fifty mm is slightly larger than CDFG’s legal size limit of 305 mm (12 inches). A 

350 mm bass is three to five years old (Schaffter, 1998; Moyle, 2002). 

4.8.2 Correlations between Standard 350 mm and All Largemouth Bass Data 

Figure 4.4 presents the regression between mercury levels in standard 350-mm largemouth 

bass collected in year 2000 and weighted-average concentrations in 300-400 mm largemouth 

bass collected between 1998 and 2000 in five delta subareas26 (Table 4.10). Each data point 

represents one subarea. The correlation is statistically significant (P<0.01) and has a slope of 

0.8, suggesting that mercury concentrations do not vary appreciably between the two groups. 

The results suggest that year 2000 standard 350-mm bass mercury levels are representative of 

mercury concentrations in largemouth bass collected between 1998 and 2000. 

4.8.3 Largemouth Bass/Trophic Level Food Group Comparisons 

Regressions between mercury concentrations in standard 350-mm largemouth bass and TL3 

and TL4 food groups are presented in Figure 4.5. The purpose of this analysis was to 

determine whether consistent relationships might exist between the different assemblages of 

fish and, if so, whether it might be possible to describe safe mercury ingestion rates for wildlife 

species and humans in terms of the mercury concentration in a standard 350-mm largemouth 

bass. The relationships were evaluated using linear, exponential, logarithmic, and power 

curves; in each but one case the type of curve that provided the highest R2

 value was 

selected.27 All of the correlations were statistically significant (P<0.05 or less). The regressions 

 

26 Data collected in 1998-2000 contained individual and composite samples. Mercury concentrations in the 

composite samples were weighted by number of individual fish in the composite and then averaged with individual 

results. 27 A logarithmic curve best fits the points comparing standard 350-mm largemouth bass mercury concentrations to 

150-500 mm TL4 fish (Figure 4.3). However, the curve intercepts the x-axis well above zero, preventing the 

prediction of standard largemouth bass mercury concentrations that corresponds to the range of alternative large 

TL4 fish mercury targets developed for human protection (0.58, 0.29, 0.24 and 0.05 mg/kg). This is also true of a 

linear curve: it intercepts the x-axis above zero. Therefore, a linear equation with the intercept set to zero was used 

to estimate standard 350-mm largemouth bass mercury concentrations that correspond to the preferred and 

alternative large TL4 fish targets. All three regressions are statistically significant (P<0.01). Use of either the linear 

or logarithmic curves to predict safe levels for largemouth bass that correspond to the TL4 target alternatives has 

additional uncertainty because two of the alternatives (0.24 and 0.05 mg/kg) are lower than the lowest of observed 

values (0.26 mg/kg in the Central Delta subarea) upon which the curves are based. 

Delta Methylmercury TMDL Report 59 April 2010 
demonstrate that there are predictable relationships between mercury concentrations in 

standard 350-mm largemouth bass and all trophic level food groups in the Delta. 

Table 4.9 presents the predicted safe dietary mercury concentrations for each TLFG target in 

terms of standard 350-mm bass. The safe largemouth bass mercury levels were calculated 

from the regression equations in Figure 4.5. The lowest largemouth bass mercury value 

(0.24 mg/kg) corresponds to 0.08 mg/kg in 150-500 mm TL3 fish. This is the most conservative 

of all the calculated largemouth bass safe levels and, if attained, should fully protect all listed 

beneficial uses in the Delta. Staff recommends that 0.24 mg/kg, wet weight, in a standard 

350-mm largemouth bass be used as an implementation goal in the linkage analysis 

(Chapter 5) and determination of methylmercury allocations (Chapter 8). 

As described in Tables 4.8 and 4.11, percent reductions in fish methylmercury levels ranging 

between 0 and 77% will be needed to meet the recommended numeric targets for large and 

small TL3 and TL4 fish and the implementation goal for standard 350-mm largemouth bass in 

the different Delta subareas. Staff expects that when methylmercury concentrations in 

largemouth bass reach the recommended implementation goal for standard 350-mm 

largemouth bass, then concentrations in other aquatic organisms also will have declined 

sufficiently to protect human and wildlife consumers. Monitoring should be conducted in all 

trophic level food groups at that time to verify that the expected decreases have occurred. 

Key points and options to consider for the numeric targets are listed after Figure 4.5. 

Table 4.10: Mercury Concentrations in Standard 350-mm and 300-400 mm Largemouth Bass 

Hg Concentrations (mg/kg) by Delta Subarea 

Central

Delta 

Mokelumne 

River 

Sacramento

River 

San Joaquin 

River 

West 

Delta 

Year 2000 Standard 350-mm largemouth bass 

collected in September/October 2000 (a) 0.19 1.04 0.72 0.68 0.31 

300-400 mm largemouth bass collected 

between 1998 and 2000 (b) 0.31 0.94 0.76 0.64 0.30 

(a) The standard 350-mm largemouth bass mercury concentrations are predicted values derived using the regressions in 

Figure 4.3. 

(b) The values for the 300-400 mm bass are weighted-average concentrations in 300-400 mm largemouth bass collected 

between 1998 and 2000 from multiple locations within each of the five delta subareas. 

Table 4.11: Percent Reductions in Standard 350-mm Largemouth Bass Methylmercury Levels Needed 

to Meet the Recommended Implementation Goal of 0.24 mg/kg in Each Delta Subarea.

Central Delta Mokelumne River Sacramento River San Joaquin River West Delta 

0% 77% 67% 65% 23% 

Delta Methylmercury TMDL Report 60 April 2010 
Mokelumne River (Interstate 5)

y = 7E-07x 2.4267

R2 = 0.8704

0.0

0.5

1.0

1.5

0 100 200 300 400 500 600

Length (mm)

Mercury Concentration 

(mg/kg)

Central Delta (Mildred Island)

y = 1E-05x 1.68

R2 = 0.6405

0.0

0.5

1.0

1.5

0 100 200 300 400 500 600

Length (mm)

Mercury Concentration 

(mg/kg)

1.04

0.19

Sacramento River (RM44/Isleton)

y = 1E-08x 3.0891

R2 = 0.7791

0.0

0.5

1.0

1.5

0 100 200 300 400 500 600

Length (mm)

Mercury Concentration 

(mg/kg)

San Joaquin River (Vernalis)

y = 5E-06x 2.0184

R2 = 0.6935

0.0

0.5

1.0

1.5

0 100 200 300 400 500 600

Length (mm)

Mercury Concentration 

(mg/kg)

0.72 0.68

W est Delta (Sherman Lake)

y = 0.0318e0.0065x

R2 = 0.6249

0.0

0.5

1.0

1.5

0 100 200 300 400 500 600

Length (mm)

Mercury Concentration 

(mg/kg)

Figure 4.3: Site-specific Relationship between Largemouth Bass Length and Mercury Concentrations in 

the Delta. The relationships were used to predict the mercury content 

of a standard, 350-mm length bass sampled in September/October 2000, as indicated 

by the dashed lines. All relationships were significant at least at P<0.05. 

0.31

Delta Methylmercury TMDL Report 61 April 2010 
y = 0.8062x + 0.116

R2

 = 0.97

0.0

0.4

0.8

1.2

0.0 0.4 0.8 1.2

2000 Standard 350 m m LMB Hg (m g/kg)

1998-2000 Wtd Ave 300-400 m m

LMB Hg Conc (m g/kg)

Figure 4.4: Comparison of Mercury Levels in 

Standard 350 mm Largemouth Bass (LMB) 

Collected at Linkage Sites in 2000 and 

 Mercury Levels in 300-400 mm LMB 

Collected throughout Each Subarea in 1998-2000. 

Delta Methylmercury TMDL Report 62 April 2010 
 Figure 4.5: Comparison of Mercury Concentrations in Standard 350-mm Largemouth Bass (LMB) Caught 

in September/October 2000 and Composites of Fish from Various 

Trophic Level (TL) Food Groups Caught between 1998 and 2001. 

The regressions are used to predict safe diets for target species listed in Table 4.9 in terms of largemouth 

bass mercury concentrations. Note, the recommended target for large TL4 fish (0.24 mg/kg) developed 

for human protection is lower than average mercury levels observed in the Delta, resulting in a 

corresponding standard 350-mm largemouth bass concentration that falls slightly below the 

regression curve based on observed values. 

Osprey Target [150-350 mm TL4 Fish]

y = 0.647Ln(x) + 1.2329

R2 = 0.999

0.0

0.4

0.8

1.2

0.0 0.2 0.4 0.6 0.8

TL Food Group Hg Conc (mg/kg)

LMB Hg Conc (mg/kg)

0.26

0.36

Human Target [150-500 mm TL3 Fish]

y = 0.6075Ln(x) + 1.7706

R2 = 0.8297

0.0

0.4

0.8

1.2

0.0 0.1 0.2 0.3

TL Food Group Hg Conc (mg/kg)

LMB Hg Conc (mg/kg)

0.08

0.24

Grebe Target [150-350 mm TL3 Fish]

y = 0.5905Ln(x) + 1.7983

R2 = 0.9464

0.0

0.4

0.8

1.2

0.0 0.1 0.2 0.3

TL Food Group Hg Conc (mg/kg)

LMB Hg Conc (mg/kg)

0.08

0.31

Kingfisher Target [50-150 mm TL2-3 Fish]

y = 0.7134Ln(x) + 2.8654

R2 = 0.8462

0.0

0.4

0.8

1.2

0.00 0.02 0.04 0.06 0.08 0.10

TL Food Group Hg Conc (mg/kg)

LMB Hg Conc (mg/kg)

0.05

0.73

Least Tern Target [<50 mm TL2 Fish]

y = 0.7642Ln(x) + 3.0996

R2 = 0.7759

0.0

0.4

0.8

1.2

0.00 0.02 0.04 0.06 0.08

TL Food Group Hg Conc (mg/kg)

LMB Hg Conc (mg/kg)

0.03

0.41

Human Target [150-500 mm TL4 Fish]

y = 1.1725x

R2 = 0.9322

0.0

0.4

0.8

1.2

0.0 0.4 0.8

TL Food Group Hg Conc (mg/kg)

LMB Hg Conc (mg/kg)

0.24

0.28

Delta Methylmercury TMDL Report 63 April 2010 
Key Points 

• The concentration of methylmercury in fish tissue is the numeric target selected for the Delta 

methylmercury TMDL. Measurements of mercury in fish should be able to assess whether 

beneficial uses are being met because fish-eating (piscivorous) birds and mammals are 

most likely at risk for mercury toxicity. 

• Piscivorous species identified in the Delta are: American mink, river otter, bald eagle, 

kingfisher, osprey, western grebe, common merganser, peregrine falcon, double crested 

cormorant, California least tern, and western snowy plover. Bald eagles, California least 

terns and peregrine falcons are listed by the State of California or by USFWS as either 

threatened or endangered species. 

• Acceptable fish tissue levels of mercury for the trophic level food groups consumed by each 

wildlife species were calculated using the method developed by USFWS that addresses daily 

intake levels, body weights and consumption rates. Numeric targets were developed to 

protect humans in a manner analogous to targets for wildlife using USEPA-approved 

methods and regional information. 

• Central Valley Water Board staff recommends two numeric targets for large fish: 0.24 mg/kg 

(wet weight) in muscle tissue of large trophic level four (TL4) fish such as bass and catfish 

and 0.08 mg/kg (wet weight) in muscle tissue of large TL3 fish such as carp and salmon. 

These targets are protective of (a) humans eating 32 g/day (1 meal/week) of commonly 

consumed, large fish; and (b) all wildlife species that consume large fish. The evaluation of 

the relationships between methylmercury concentrations in large TL4 fish and the other 

trophic level food groups indicated that wildlife species that consume smaller or lower trophic 

level fish would be protected by the large TL3 and TL4 fish targets developed for human 

protection. 

• To ensure that wildlife species dining only on small fish are protected, staff proposes an 

additional target of 0.03 mg/kg methylmercury in whole TL2 and 3 fish less than 50 mm in 

length. This target represents the safe mercury level for prey consumed by the California 

least tern, a piscivorous species listed by the federal government as endangered. Such a 

target for small fish also would protect the Western snowy plover and other species that 

consume small fish. 

• Elevated fish mercury concentrations occur along the periphery of the Delta while lower body 

burdens are measured in the central Delta. Percent reductions in fish methylmercury levels 

ranging from 0% to 74% will be needed to meet the numeric targets for wildlife and human 

health protection in all subareas of the Delta. 

• The relationships between methylmercury concentrations in largemouth bass and the trophic 

level food groups also were examined because largemouth bass are a good bioindicator 

species and only largemouth bass data are available for the same sampling period and 

locations as the methylmercury water data available for the linkage analysis (next chapter). 

It was possible to describe safe mercury ingestion rates for wildlife species and humans in 

terms of the mercury concentration in a standard 350-mm largemouth bass. A 

methylmercury concentration of 0.24 mg/kg in 350-mm length largemouth bass would fully 

protect humans and piscivorous wildlife species and is proposed as an implementation goal 

for use in the linkage analysis and determination of methylmercury allocations for point and 

nonpoint sources. 

Delta Methylmercury TMDL Report 64 April 2010 
Options to Consider 

• A variety of assumptions can be made to calculate safe fish mercury levels for humans. For 

example, staff recommended targets of 0.08 mg/kg and 0.24 mg/kg for large TL3 and TL4 

fish, respectively, because such targets are protective of a higher consumption rate (~1 meal 

per week) than that used to develop the USEPA criterion (~1 meal per 2 weeks) and 

because available information indicates that anglers take home a mixture of TL3 and TL4 

species. Application of the USEPA criterion to large TL4 fish results in a target of 

0.29 mg/kg. Use of the USEPA default consumption rates of fish from TL2 (21.7%), TL3 

(45.7%) and TL4 (32.6%) produces a much higher target of 0.58 mg/kg for large TL4 fish. 

However, as the evaluations of trophic level food group and standard 350-mm largemouth 

bass mercury levels indicate, a target of 0.58 mg/kg for large TL4 fish would not protect 

several piscivorous wildlife species, such as bald eagle, osprey, river otter, grebe, 

merganser, and least tern. Large TL4 fish targets of 0.29, 0.24, or 0.05 mg/kg would be 

protective of these species. However, a large TL4 fish target of 0.05 mg/kg may not be 

attainable because it is well below regional background fish mercury levels observed in the 

western United States. 

Delta Methylmercury TMDL Report 65 April 2010 
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. 

Delta Methylmercury TMDL Report 66 April 2010 
5 LINKAGE ANALYSIS 

The Delta linkage analysis focuses on the comparison of methylmercury concentrations in water 

and biota. As discussed in Chapter 2, methylmercury is the form of mercury that 

bioaccumulates in the food web. The relationship has not previously been evaluated in the 

Delta, but statistically significant, positive correlations have been reported between aqueous 

methylmercury and aquatic biota elsewhere (Brumbaugh et al., 2001; Foe et al., 2002; 

Slotton et al., 2003; Tetra Tech, Inc., 2005a; Sveinsdottir and Mason, 2005), indicating that 

methylmercury concentrations in water are one of the primary factors determining 

methylmercury concentrations in fish. This linkage analysis develops a Delta-specific 

mathematical relationship between aqueous and biotic methylmercury concentrations. The 

relationship is used to determine an aqueous methylmercury goal that, if met, is predicted to 

produce safe fish tissue levels for both human and wildlife consumption (Chapter 4). The 

aqueous methylmercury goal is then used to allocate methylmercury reductions for within-Delta 

and tributary sources (Chapter 8). 

The linkage analysis has three sections. The first section describes the available fish and 

aqueous methylmercury data. The second section illustrates the mathematical relationship 

between unfiltered water and largemouth bass methylmercury levels. The mathematical 

relationship is used to develop an unfiltered aqueous methylmercury goal of 0.06 ng/l that 

corresponds to the recommended fish tissue targets that are protective of humans and wildlife 

that consume Delta fish. The final section provides an alternate linkage using 0.45 μ filtered 

methylmercury water data. Results of these correlation-based linkages are comparable to 

results of more empirical linkage methods, such as the evaluation of Delta areas that currently 

achieve the implementation goal for largemouth bass, and the use of bioaccumulation factors to 

calculate an aqueous methylmercury goal. 

5.1 Data Used in Linkage Analysis 

Fish. Water and fish have not been sampled in the Delta for the specific purpose of developing 

a linkage analysis. As a result, there is an acceptable overlap for only a portion of the available 

fish and water data. This linkage analysis focuses on recently collected largemouth bass data 

for several reasons. First, largemouth bass was the only species systematically collected near 

many of the aqueous methylmercury sampling locations used to develop the methylmercury 

mass balance for the Delta (next section). Second, largemouth bass are piscivorous and have 

some of the highest mercury levels of any fish species evaluated in the Delta. Third, bass are 

abundant and widely distributed throughout the Delta. Fourth, bass have high site fidelity. That 

is, largemouth bass maintain a localized home range; most stay within a mile of a given 

waterway (Davis et al., 2003). Such high site fidelity makes them useful bioindicators of spatial 

variation in mercury accumulation in the aquatic food chain. Finally, spatial trends across the 

Delta in standard 350-mm largemouth bass mercury levels are representative of spatial trends 

in the trophic level food group mercury levels (Section 4.7). Largemouth bass were collected 

from 19 locations in the Delta in August/September 1998, 26 locations in September/October 

1999, and 22 locations in September/October 2000 (Davis et al., 2000; Davis et al., 2003; LWA, 

2003). The year 2000 largemouth bass data were used in the linkage analysis because the 

Delta Methylmercury TMDL Report 67 April 2010 
exposure period of these fish had the greatest overlap with the available water data. Monthly 

water data were collected during the last eight months of the life of the fish. Figure 5.1 shows 

the water and largemouth bass methylmercury sampling locations used in the linkage analysis. 

The mercury concentrations in standard 350-mm largemouth bass and the corresponding water 

data for each sampling location are presented in Table 5.1. Section 4.8 in Chapter 4 describes 

the method used to calculate standard 350-mm largemouth bass mercury concentrations.

Water. Unfiltered methylmercury water samples were collected periodically between March 

2000 and April 2004 at multiple Delta locations (Figure 5.1, Tables D.1 and D.3 in Appendix D). 

The monthly March-October 200028 subset of this data has the greatest overlap with the 

lifespan of the largemouth bass sampled in September/October 2000. The March-October 20

and March 2000 to April 2004 data were pooled by Delta subarea to calculate monthly averag

(Tables D.2 and D.3).

00 

es 

29 These values were used to estimate average and median 

methylmercury concentrations for the March-October 2000 period and annual and seasonal 

average and median concentrations for the March 2000 to April 2004 period (Table 5.1).30 

Table 5.1: Fish and Water Methylmercury Values by Delta Subarea. 

Delta Subarea (a)

Sacramento 

River 

Mokelumne 

River 

Central 

Delta 

San Joaquin 

River 

West 

Delta 

FISH [Sampled in September/October 2000] (mg/kg)

Standardized 350-mm 

Largemouth Bass 0.72 1.04 0.19 0.68 0.31 

WATER [Sampled between March and October 2000] (ng/l)

Average 0.120 0.140 0.055 0.147 0.087 

Median 0.086 0.142 0.032 0.144 0.053 

WATER [Sampled between March 2000 and April 2004] (ng/l)

Annual Average 0.108 0.166 0.060 0.160 0.083 

Annual Median 0.101 0.161 0.051 0.165 0.061 

Cool Season Average (b) 0.137 0.221 0.087 0.172 0.106 

Cool Season Median 0.138 0.246 0.077 0.175 0.095 

Warm Season Average 0.094 0.146 0.050 0.156 0.075 

Warm Season Median 0.089 0.146 0.040 0.162 0.055 

(a) See Figure 5.1 for the location of each water and fish collection site. 

(b) For this analysis, “cool season” is defined as November through February and “warm season” is 

defined as March through October. 

 

28 Coincidentally, March through October defines the season with warmer water temperatures. Aquatic biota may be 

more metabolically active and have a higher methylmercury bioaccumulation rate in summer. In addition, sulfatereducing bacteria may have higher methylmercury production rates making this a critical bioaccumulation period. 29 The methylmercury concentrations for two periods – (a) March-October 2000 and (b) September 2000 to April 

2004 – were compared at each sampling location in Figure 5.1 with a paired t-test to determine whether the mean 

concentrations for the two time periods were different. The tests indicated no significant difference (P ≤ 0.05) for 

any location. Therefore, the data for March 2000 to April 2004 (a substantially larger database than that for 

March-October 2000) were also evaluated in the linkage analysis. 30 Monthly averages were used to ensure that the seasonal and annual values were not biased by months with 

different sample sizes. 

Delta Methylmercury TMDL Report 68 April 2010 
Figure 5.1: Aqueous and Largemouth Bass Methylmercury Sampling Locations Used 

in the Linkage Analysis. 

Delta Methylmercury TMDL Report 69 April 2010 
5.2 Bass/Water Methylmercury Regressions & Calculation of Aqueous 

re 

sions 

sue 

icted by the regression based on average cool season water 

in aquatic 

y. 

ows the ambient water methylmercury levels 

ere 

ations above the minimum reporting level of 0.05 ng/l and thus can be 

quantified accurately. 

Methylmercury Goal 

The mercury concentrations in standard 350-mm largemouth bass for each Delta subarea we

regressed against the average and median unfiltered aqueous methylmercury levels for the 

March to October 2000 and March 2000 to April 2004 periods to determine whether 

relationships might exist (Figure 5.2, Table 5.2, and Figure D.1 in Appendix D). The regres

were evaluated using linear, exponential, logarithmic, and power curves. Power curves 

provided the best fit, although all the regression types demonstrated a positive relationship 

between aqueous and biotic methylmercury concentrations. In each scenario described by 

Table 5.2, increasing the aqueous methylmercury concentration results in increasing fish tis

levels. The recommended implementation goal for fish methylmercury in the Delta is 0.24 

mg/kg (wet weight) in a standard 350-mm largemouth bass (Chapter 4). Substitution of 

0.24 mg/kg into the equations in Table 5.2 results in predicted average and median safe water 

methylmercury values that range from 0.04 to 0.09 ng/l. The lowest concentration is predicted

by the regression based on median March to October 2000 water values (Scenario 1B) while 

the highest concentration is pred

concentrations (Scenario 3A). 

Staff recommends that 0.06 ng/l methylmercury in unfiltered water be used as an 

implementation goal for the determination of load allocations (Chapter 8). This 

recommendation is based on Scenario 1A in Table 5.2 and incorporates an explicit margin of 

safety of about 10%. The goal could be applied as an annual average methylmercury 

concentration. Staff recommends this value because only the March to October 2000 period 

overlapped the lifespan of the largemouth bass analyzed for mercury body burden. Also, little is 

known about the seasonal exposure regime controlling methylmercury concentrations 

biota. Therefore, an annual average was selected as it weights all seasons equall

The recommended implementation goals for largemouth bass and ambient water 

methylmercury in the Delta are based on Scenario B.4 from Table 4.5 in Chapter 4. 

Scenarios A.1, A.4, B.4 and E.3 are evaluated as fish tissue objective alternatives in the draft 

Basin Plan Amendment staff report. Table 5.3 sh

that correspond to all the objective alternatives. 

Progress towards attaining Alternative 5 in Table 5.3 would be difficult to track. This is because

Alternative 5 (0.05 mg/kg in large TL4 fish) is substantially below existing conditions anywh

in the Delta, thus making it difficult to accurately extrapolate from methylmercury in fish to

corresponding methylmercury in water. Such extrapolation for Alternative 5 produces a 

concentration of 0.028 ng/l methylmercury in water, which is below the current minimum 

reporting level for laboratory analyses for methylmercury. (Minimum reporting levels are 

equivalent to the lowest calibration standard for methylmercury, which is currently 0.05 ng/l.) 

Though water methylmercury concentrations below the minimum reporting level can be 

detected, they cannot be quantified accurately; thus, Alternative 5 progress would be difficult to

quantify and track. The other fish tissue objective alternatives correspond to water 

methylmercury concentr

Delta Methylmercury TMDL Report 70 April 2010 
To evaluate the bass/water methylmercury relationship, staff used measures of central tendency 

for the fish and water concentration variables. Because a fish integrates methylmercury that is 

taken in over its lifetime, it is not valid biologically to match individual fish and water samples for 

the purposes of graphing them, when other data are available. An average of the aqueous 

methylmercury concentrations collected over an eight-month period better represents aqueous 

methylmercury available to the fish, than do single water samples. The fish tissue 

concentrations used in Figures 5.2 and 5.3 are the methylmercury concentrations in a singlesize (standard 350 mm) largemouth bass that staff calculated using data from bass of various 

sizes in each subarea. Because methylmercury concentrations vary with size of fish, 

calculating the expected methylmercury fish level in a single length of fish is a common practice 

for comparing fish methylmercury concentrations between locations without the confounding 

effect of size difference (see Chapter 4 for a description of the standardization method). 

The linkage analysis for the Delta relies upon sequential correlations to determine the numerical 

aqueous methylmercury goal. A potential problem with the analysis is that each correlation has 

an associated error term. No attempt has been made to estimate these errors and propagate 

them from one correlation to the next when calculating the recommended aqueous 

methylmercury goal. 

Staff determined the statistical strength of each regression equation (shown on Figures 5.2 

and 5.3) for the purpose of selecting the variables that exhibited the strongest relationship 

(average versus median aqueous methylmercury and filtered versus unfiltered methylmercury). 

Staff noted that the regression for standard 350 mm largemouth bass and average unfiltered 

methylmercury has the highest R2

 value. However, staff did not rely on the statistical 

significance to support the fish/methylmercury linkage analysis. Multiple studies assert that the 

supply of aqueous methylmercury is a key determining factor in the concentrations of 

methylmercury in biota (Brumbaugh et al., 2001; Paterson et al., 1998; SFBRWQCB, 2008; 

Slotton et al., 2004; Stewart et al., 2008; St. Louis et al, 2004; Wiener et al., 2003). As 

described below, staff evaluated two other approaches to determining an aqueous 

methylmercury goal and obtained results similar to that produced by the quantitative relationship 

in Figure 5.2. 

There are two alternate, more empirical, approaches. The first approach is to compare existing 

largemouth bass and aqueous methylmercury levels to the proposed implementation goals. 

The average March-October 2000 methylmercury concentration in the Central Delta (0.055 ng/l, 

Table 5.1) is less than the proposed aqueous goal of 0.06 ng/l while concentrations in the West 

Delta (0.087 ng/l) are higher. Similarly, the methylmercury concentration in standard 350-mm 

bass in the Central Delta is 0.19 mg/kg while the concentration in the West Delta is 0.31 mg/kg 

(Table 4.10). The recommended implementation goal is 0.24 mg/kg in standard 350-mm 

largemouth bass. Therefore, empirical observations suggest that the “correct” aqueous 

methylmercury goal to achieve safe mercury levels in the various trophic level food groups must 

lie between 0.055 and 0.087 ng/l. If the aqueous methylmercury goal of 0.06 ng/l is attained in 

the Delta, then methylmercury concentrations in all trophic level food groups are predicted to fall 

within the safe tissue concentration range. 

A second linkage approach that does not rely on the correlation between largemouth bass and 

water methylmercury concentrations to derive an implementation goal for water makes use of 

Delta Methylmercury TMDL Report 71 April 2010 
Delta Methylmercury TMDL Report 72 April 2010 

 

bioaccumulation factors (BAFs), an approach used in numerous USEPA-approved TMDLs 

across the country.31 A BAF is the ratio of the concentration of a chemical in fish tissue to the 

concentration of the chemical in the water column. As defined in the Mercury Study Report to 

Congress (USEPA, 1997a), the BAF is the concentration of the methylmercury in fish divided by 

the concentration of dissolved methylmercury in water. A total BAF based on the total 

concentration of a chemical in water also can be used (USEPA, 2003). By definition, BAFs 

imply a linear relationship between methylmercury in the water column and in fish. Section D.2 

in Appendix D describes the method used to develop BAF-based implementation goals for the 

Delta and its subareas using standard 350-mm largemouth bass and average aqueous 

methylmercury concentrations. The resulting safe aqueous methylmercury levels ranged from 

0.029 to 0.069 ng/l, and averaged 0.052 ng/l: 

31 Refer to: http://www.epa.gov/OWOW/tmdl/index.html. 

• Central Delta subarea: 0.069 ng/l; 

• Mokelumne River subarea: 0.032 ng/l; 

• Sacramento River subarea: 0.040 ng/l; 

• San Joaquin River subarea: 0.052 ng/l; 

and 

• West Delta subarea: 0.067 ng/l. 

These levels are slightly less than but comparable to the safe levels produced using the 

regression-based approach. The similarity most likely occurs because both methods used the 

same fish and water data, and because the regression described in Figure 5.2(A) is nearly 

linear at low fish and water methylmercury levels. This approach has the benefit that it does not 

assume identical bioaccumulation rates across the Delta. However, unlike the regressionbased method, the BAFs inherently assume a linear relationship between fish and water 

methylmercury levels. 

The points on the graphs in Figures 5.2 and 5.3 essentially represent methylmercury 

bioaccumulation factors (BAFs) for each Delta subarea. The regression equations demonstrate 

that for all of the Delta subareas, the average aqueous methylmercury concentration accounts 

for a very large part of the difference between fish mercury concentrations. The strong 

correlation shown in Figure 5.2 between Delta subarea BAFs is a strength of this TMDL’s 

linkage analysis approach and underlies the feasibility of reaching the fish tissue targets. 

The safe aqueous methylmercury concentrations predicted for the Delta are comparable to 

analysis results for Cache Creek and nationwide studies. Brumbaugh and others (2001) found 

in a national survey of 106 stations from 21 basins that one-time unfiltered methylmercury water 

samples collected during the fall season were also positively correlated with largemouth bass 

tissue levels. An aqueous methylmercury concentration of 0.058 ng/l was predicted to produce 

three-year old largemouth bass (262-mm average length fish) with 0.3 mg/kg mercury tissue 

concentration. In the Cache Creek watershed, an unfiltered methylmercury concentration of 

0.14 ng/l corresponded with the production of 0.23 mg/kg mercury in large fish (Cooke et al., 

2004). Predicted safe methylmercury water values for the Delta are bracketed by safe water 

concentrations determined by the national and Cache Creek studies. 
Additional fish and methylmercury water studies that address uncertainties in the linkage 

analysis are planned. These include additional evaluations of standard 350-mm largemouth 

bass tissue concentrations at more locations in the Delta and elsewhere in the Central Valley 

after multiple years of aqueous methylmercury data have been obtained. Studies also are 

planned to better determine the seasonal exposure regime when most of the methylmercury is 

sequestered in the aquatic food chain. Board staff will work with a statistician to develop a more 

powerful statistical analysis of the linkage during the study period. The results of these studies 

may lead to future revisions in the proposed aqueous methylmercury goal. 

A. LMB vs. Average Aqueous MeHg

y = 20.365x1.6374

R2 = 0.91

0.0

0.5

1.0

1.5

0.00 0.05 0.10 0.15 0.20

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

B. LMB vs. Median Aqueous MeHg

y = 6.6501x1.0189

R2 = 0.90

0.0

0.5

1.0

1.5

0.00 0.05 0.10 0.15 0.20

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

0.24

0.038

Figure 5.2: Relationships between Standard 350-mm Largemouth Bass Methylmercury 

and March to October 2000 Unfiltered Aqueous Methylmercury. 

The proposed implementation goal for standard 350-mm largemouth bass is 0.24 mg/kg. 

0.24

0.066

Table 5.2: Relationships between Methylmercury Concentrations in Water and Standard 350-mm 

Largemouth Bass 

Aqueous MeHg Data Period Scenario 

Regression 

Equation R2 (a)

Aqueous MeHg Conc. (ng/l) 

Corresponding to 

LMB value of 0.24 mg/kg 

A. Average Aqueous MeHg y = 20.365x1.6374 0.91 0.066 1. March to October 2000 

B. Median Aqueous MeHg y = 6.6501x1.0189 0.90 0.038 

A. Average Aqueous MeHg y = 14.381x1.51 2. March 2000 to April 2004 0.88 0.066 

 - Annual - B. Median Aqueous MeHg y = 8.0903x1.1926 0.86 0.052 

A. Average Aqueous MeHg y = 17.795x1.8007 3. March 2000 to April 2004 0.90 0.092 

 - Cool Season - B. Median Aqueous MeHg y = 8.8725x1.4347 0.92 0.081 

A. Average Aqueous MeHg y = 11.528x1.339 4. March 2000 to April 2004 0.83 0.055 

 - Warm Season - B. Median Aqueous MeHg y = 6.8941x1.0723 0.85 0.044 

(a) All R2 values are statistically significant at P<0.05. Regression graphs are provided in Figure 5.2 and Appendix D. 

Delta Methylmercury TMDL Report 73 April 2010 
Table 5.3. Ambient Water Methylmercury Concentrations that Correspond to Alternative Fish Tissue 

Objectives Evaluated in the Basin Plan Amendment Staff Report. 

Fish Tissue 

Objective 

Alternative (a)

Scenario # 

from 

Table 4.5 

150-

500 mm 

TL3 Fish 

Tissue 

Target 

(mg/kg)

150-

500 mm

TL4 Fish

Tissue

Target

(mg/kg)

Predicted 

Standard 350-mm 

Largemouth Bass 

(LMB) MeHg 

Concentration for 

TL3 Fish Target 

(mg/kg) (b)

Predicted 

Standard 350-mm 

LMB MeHg 

Concentration for 

TL3 Fish Target 

(mg/kg) (b)

Ambient Water 

MeHg Concentration 

that Corresponds to 

the Lowest 

Predicted LMB 

Concentration for 

the Alternative 

(ng/l) (b)

2 A.1 0.20 0.58 0.79 0.68 0.125 

3 A.5 - - - 0.29 0.34 0.082 

4 B.4 0.08 0.24 0.24 0.28 0.066 

5 E.3 - - - 0.05 0.06 0.028 

(a) Alternative numbers from Table 3.1 in the Basin Plan Amendment Staff Report. “Alternative 1” is the “no action” alternative and 

has a narrative objective rather than a numeric objective. 

(b) Predicted standard 350-mm largemouth bass methylmercury concentrations that correspond to the TL3 fish targets were 

calculated using the equation provided in Figure 4.5 for “Human Target [150-500 TL3 Fish]”. Predicted standard 350-mm 

largemouth bass methylmercury concentrations that correspond to the TL4 fish targets are based on the equation provided in 

Figure 4.5 for “Human Target [150-500 TL4 Fish]”. 

(c) Ambient water methylmercury concentrations that correspond to the predicted largemouth bass concentrations were calculated 

using the equation for Scenario 1A in Table 5.2. 

 

5.3 Evaluation of a Filtered Aqueous Methylmercury Linkage Analysis 

This section presents an alternate linkage analysis based on filter-passing32 aqueous 

methylmercury data. Methylmercury concentrations in standard 350-mm largemouth bass for 

each Delta subarea (Table 5.1) were regressed against the average and median filtered 

aqueous methylmercury levels for March-October 2000 (Table 5.4 and Table D.4 in 

Appendix D). Figure 5.3 demonstrates that there is a statistically significant positive correlation 

between filter-passing aqueous and largemouth bass tissue methylmercury levels. However, 

average and median filter-passing methylmercury water values for the Central Delta and 

Western Delta, regions that define the lower end of the regression, are determined mainly by 

values lower than the method detection limit (0.022 ng/l). Furthermore, substitution of the 

recommended implementation goal of 0.24 mg/kg mercury for 350 mm largemouth bass in the 

equations in Figure 5.3 results in predicted average and median safe water values (0.016 ng/l 

and 0.010 ng/l, respectively) below the method detection limit. Similarly low levels resulted 

when the BAF-based linkage method was used (see Section D.2 in Appendix D). Staff does not 

recommend adoption of a methylmercury goal that is unquantifiable with present analytical 

methods. 

Key points to consider for the linkage analysis are listed after Table 5.4 and Figure 5.3. 

 

32 Water samples were filtered using 0.45-micrometer capsule filters. Much of the methylmercury measured in 

filtered samples is colloidal (Choe, 2002). Hence the results are called “filter-passing” rather than “dissolved”. 

Delta Methylmercury TMDL Report 74 April 2010 
Table 5.4: Average and Median Filtered Methylmercury Concentrations (ng/l) 

for March 2000 to October 2000 for Each Delta Subarea. 

Delta Subarea (a)

Sacramento 

River 

Mokelumne 

River 

Central 

Delta 

San Joaquin 

River 

West 

Delta 

Average 0.043 0.078 0.029 0.037 0.019 

Median 0.039 0.069 0.014 0.036 0.011 

(a) See Figure 5.1 for the location of each water and fish collection site. See Appendix L for raw data 

and Table D.4 in Appendix D for monthly averages, upon which these average and median values 

are based. 

LMB vs. Median Filtered Aqueous MeHg

y = 14.358x + 0.1059

R2 = 0.95

0.0

0.5

1.0

1.5

0.00 0.03 0.06 0.09

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

LMB vs. Average Filtered Aqueous MeHg

y = 13.725x + 0.0214

R2 = 0.80

0.0

0.5

1.0

1.5

0.00 0.03 0.06 0.09

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

Figure 5.3: Relationships between Standard 350-mm Largemouth Bass Mercury Levels 

and March to October 2000 Filtered Aqueous Methylmercury. 

Key Points 

• Statistically significant mathematical relationships exist between unfiltered and filter-passing 

methylmercury concentrations in water and fish tissue. 

• Based on the relationship between average March to October 2000 unfiltered methylmercury 

concentrations in water and methylmercury in standard 350-mm largemouth bass tissue, 

staff recommends an implementation goal for ambient Delta waters of 0.06 ng/l unfiltered 

methylmercury. The proposed goal incorporates an explicit margin of safety of about 10%. 

Staff recommends that the goal be applied as an annual average methylmercury 

concentration. 

• More empirical linkage methods, such as the evaluation of Delta areas that currently achieve 

the implementation goal for largemouth bass and the use of bioaccumulation factors to 

calculate an aqueous methylmercury goal, predict safe aqueous methylmercury levels 

comparable to the correlation-based linkage method. 

Delta Methylmercury TMDL Report 75 April 2010 
Delta Methylmercury TMDL Report 76 April 2010 

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6 SOURCE ASSESSMENT – METHYLMERCURY 

The Delta mercury TMDL program addresses the sources of two constituents, methyl and total 

mercury. The program focuses on methylmercury because, as described in Chapters 2 and 5, 

methylmercury is the form of mercury that bioaccumulates in the Delta food web and statistically 

significant, positive correlations have been found between aqueous methylmercury and aquatic 

biota in the Delta and elsewhere, indicating that methylmercury concentrations in water are one 

of the primary factors determining methylmercury concentrations in fish. The program also 

addresses total mercury for several reasons: methylmercury production has been found to be a 

function of the total mercury content of sediment (Chapter 3); the mercury control program for 

the Delta must maintain compliance with the USEPA’s CTR criterion for total recoverable 

mercury in freshwater sources; and the mercury control program for San Francisco Bay has 

assigned a total mercury load reduction of 110 kg/yr to the Central Valley (Johnson and Looker, 

2004; SFBRWQCB, 2006). Sources and losses of methylmercury are described in this chapter. 

Sources and losses of total mercury and suspended sediment are described in Chapter 7. All of 

the mass load calculations are based on Equation 6.1: 

Equation 6.1: 

 Mx = Cx * V 

Where: Mx = Mass of constituent, X 

 Cx = Concentration of constituent, X, in mass per volume 

 V = Volume of water 

Average annual methylmercury loads were estimated for water years (WY) 2000 to 2003, a 

relatively dry period that encompasses the methyl and total mercury concentration data for the 

major Delta inputs and exports available at the time the TMDL was developed. As described in 

the draft Basin Plan Amendment staff report, staff recommends that a Delta mercury control 

program review take place after additional Delta-specific studies are completed, during which 

the TMDL source analysis can be updated. Staff will use data from recently completed studies, 

as well as additional information that becomes available during the next seven years, to revise 

the methylmercury source analyses as part of the program review. Although some 

methylmercury load estimates would change with incorporation of data from recent studies, the 

first implementation activities (methylmercury control studies and total mercury reductions) 

proposed for the control program (see Chapter 4 in the draft Basin Plan Amendment staff 

report) would not change. Stakeholders participating in Stakeholder Group meetings in 2009 

accepted this approach to using data that became available after the TMDL was developed. 

Section 6.1 and Appendix E describe the water volumes upon which the loads are based. 

Sections 6.2 and 6.3 describe the methylmercury concentration data for all major sources and 

sinks and identify data gaps and uncertainties. Section 6.4 reviews the results and potential 

implications of the methylmercury mass balance. Mass balances are useful because the 

difference between the sum of known inputs and exports is a measure of the uncertainty of the 

measurements and of the importance of other unknown processes at work in the Delta. 

Delta Methylmercury TMDL Report 77 April 2010 
6.1 Water Budget 

Water inputs and losses were evaluated for the WY2000-2003 period, a relatively dry period 

that encompasses the methylmercury concentration data for the major Delta inputs and exports 

available at the time the TMDL was developed (Section 6.2). In addition, the WY1984-2003 

period was evaluated to illustrate the importance of wet years, particularly for total mercury and 

sediment loading from the Yolo Bypass (Chapter 7). This 20-year period includes a mix of wet 

and dry years that is statistically similar to what has occurred in the Sacramento Basin over the 

last 100 years. An assessment of a typical distribution of wet and dry water years is critical to 

the understanding of mercury and sediment sources because, given the interannual variability in 

Sacramento Basin flows and mercury loads, and high daily loads associated with large storm 

events, the load transported by several high flow days may be equivalent to the annual load 

from the Sacramento River Basin during a dry year (see Figure E.1 and Table I.2 in 

Appendices E and I, respectively). 

Water volume information for Delta inputs and exports was obtained from a variety of sources. 

USGS and DWR gages provided daily flows for the major tributaries to the Delta. The Dayflow 

model was used to estimate daily flow to San Francisco Bay, the Delta Mendota Canal (DMC), 

and the State Water Project (SWP). The Delta Island Consumptive Use Model was used to 

estimate Delta agricultural diversion and return flows. Average annual precipitation and land 

use acreages were used to estimate wet weather inputs from urban areas, atmospheric 

deposition, and tributaries without flow gages. Project files were reviewed to determine average 

annual discharges from NPDES-permitted facilities in the Delta and annual average volumes 

removed by dredging projects. Appendix E provides a detailed description of the methods used 

to estimate annual average flow for the different water sources. 

The WY2000-2003 water budget balances within about 5%, and the WY1984-2003 water 

budget balances to within about 1% (Table 6.1). This indicates that all major water inputs and 

exports have been identified. The Sacramento River, San Joaquin River and Yolo Bypass are 

the primary water sources, with the Sacramento River providing the majority of flow. The 

primary sinks are San Francisco Bay and the state and federal pumps that transport water to 

the southern part of the State. The majority of water movement in the Delta is down the 

Sacramento River to San Francisco Bay and through a series of interconnecting channels to the 

state and federal pumps. Most of the water in winter and spring flows to San Francisco Bay, 

while in summer and fall the state and federal pumps export a larger fraction south of the Delta 

(DWR, 1995). 

6.2 Methylmercury Sources 

The following were identified as sources of methylmercury to the Delta/Yolo Bypass: tributary 

inflows from upstream watersheds, sediment flux, municipal wastewater, agricultural drainage, 

and urban runoff. Table 6.2 lists the average methylmercury concentrations and estimated 

average annual loads for each for WY2000-2003. The following sections illustrate the locations 

of the sources, describe the available methylmercury concentration data, and identify data gaps 

and uncertainties associated with the load estimates. Figures and tables cited in the text are 

arranged at the end of each source-specific section in the order in which they were mentioned. 

Delta Methylmercury TMDL Report 78 April 2010 
Table 6.1: Average Annual Water Volumes for Delta/Yolo Bypass Inputs and Losses

WY2000-2003 WY1984-2003 

Inputs & Exports Water Volume 

(M acre-feet/yr) % All Water Water Volume (M acre-feet/yr) % All Water

Tributary Sources (% of All Inputs) 

Sacramento River 15.1 75% 16.1 68% 

San Joaquin River 1.8 9.0% 3.0 13% 

Fremont Weir Spills to Yolo Bypass 1.1 5.5% 1.9 8.0% 

Mokelumne-Cosumnes River 0.43 2.4% 0.69 2.9% 

Knights Landing Ridge Cut 0.27 1.3% 0.33 1.4% 

Cache Creek Settling Basin 0.22 1.1% 0.38 1.6% 

Calaveras River 0.15 0.75% 0.16 0.68% 

French Camp Slough 0.064 0.32% 0.067 0.28% 

Willow Slough & Bypass 0.062 0.31% 0.068 0.29% 

Morrison Creek 0.061 0.30% 0.064 0.27% 

Putah Creek 0.041 0.20% 0.11 0.47% 

Ulatis Creek 0.032 0.16% 0.033 0.14% 

Bear/Mosher Creeks 0.029 0.14% 0.030 0.13% 

Dixon Area 0.012 0.06% 0.012 0.05% 

Marsh Creek (a) 0.006 0.03% 0.006 0.03% 

Other Small Drainages to Delta (b) 0.082 0.41% 0.082 0.35% 

Sum of Tributary Inputs 19.51 97.1% 23.03 97.5% 

Within-Delta Sources (% of All Inputs) 

Wastewater (Municipal & Industrial) 0.27 1.4% 0.27 1.1% 

Atmospheric (Direct) 0.089 0.45% 0.092 0.39% 

Atmospheric (Indirect) 0.16 0.80% 0.17 0.72% 

Urban 0.059 0.30% 0.061 0.26% 

Sum of Within-Delta Inputs 0.58 2.9% 0.59 2.5% 

Exports (% of All Exports) 

Outflows to San Francisco Bay [X2] 12 63% 17 73% 

State Water Project 3.2 17% 2.6 11% 

Delta Mendota Canal 2.5 13% 2.4 10% 

Agricultural Diversions (a) 0.99 5% 0.99 4.2% 

Evaporation 0.30 2% 0.3 1.3% 

Dredging (a) 0.00024 0.001% 0.00024 0.001% 

Sum of Inputs 20.09 M acre-feet 23.63 M acre-feet 

Sum of Exports 18.99 M acre-feet 23.29 M acre-feet 

Input - Export 1.10 M acre-feet 0.33 M acre-feet 

Exports / Inputs 95% 99% 

(a) Only WY2001-2003 flow data were available for Marsh Creek. Agricultural diversion volume is based on 

WY1999. The water volume removed by dredging is a 10-year average. The same water volumes for these 

inputs and exports, and for the Wastewater input, were used in both water budget periods. 

(b) “Other Small Drainages to Delta" include the following areas shown on Figure 6.1, for which methylmercury, 

total mercury and TSS concentration data are not available: Manteca-Escalon, Bethany Reservoir, Antioch, 

and Montezuma Hills areas. 

Delta Methylmercury TMDL Report 79 April 2010 
Table 6.2: Methylmercury Concentrations and Loads to the Delta/Yolo Bypass for 

WY2000-2003. 

Average 

Annual Load

(g/yr) % All MeHg

Average 

Aqueous 

Concentration

(ng/l) 

Tributary Sources 

Sacramento River @ Freeport 2,026 39% 0.10 

San Joaquin River near Vernalis 356 6.8% 0.16 

Fremont Weir Spills to Yolo Bypass 177 3.4% 0.10 

Cache Creek Settling Basin 137 2.6% 0.50 

Mokelumne River near I-5 108 2.1% 0.17 

Knights Landing Ridge Cut 100 1.9% 0.19 

Calaveras River (b) 26 0.50% 0.14 

Willow Slough & Bypass (a) 18 0.34% 0.24 

Putah Creek 11 0.21% 0.18 

Bear/Mosher Creeks (b) 11 0.21% 0.31 

French Camp Slough (b) 11 0.21% 0.14 

Ulatis Creek (b) 9.5 0.18% 0.24 

Morrison Creek (b) 7.5 0.14% 0.10 

Dixon Area (a) 3.6 0.07% 0.24 

Marsh Creek @ Highway 4 (c) 1.9 0.04% 0.25 

Other Small Drainages to Delta unknown 

Sum of Tributary Sources 3,004 58% - - - 

Within-Delta Sources 

Wetland Habitats 983 19% - - - 

Open Water Habitats 861 17% - - - 

Wastewater 205 3.9% <0.02 to 1.7 

Agricultural Lands 123 2.4% - - - 

Atmospheric Deposition 23 0.44% - - - 

Urban 20 0.38% 0.24 

Sum of Within-Delta/Yolo Bypass Sources 2,215 42% - - - 

TOTAL MeHg INPUTS: 5,219 g/yr (5.2 kg/yr)

(a) Methylmercury data were not available for Willow Slough, Willow Slough Bypass, and Dixon Area 

runoff. The average methylmercury concentration for Ulatis Creek was used to estimate their inputs 

to the Yolo Bypass because they have similar land uses as the Ulatis Creek watershed. 

(b) Average wet weather methylmercury concentrations are shown for the small watersheds rather than 

average annual concentrations. 

(c) Only WY2001-2003 flow data were available for Marsh Creek. 

Delta Methylmercury TMDL Report 80 April 2010 
Delta Methylmercury TMDL Report 81 April 2010 

6.2.1 Tributary Inputs 

Tributaries contribute almost 60% of Delta methylmercury inputs (Table 6.2) during the relatively 

dry WY2000-2003 period. Figure 6.1 illustrates the tributary watersheds that drain directly or 

indirectly to the Delta within its legal boundary. The following watershed areas drain directly to 

the Delta: 

• Calaveras, Mokelumne, Sacramento, and San Joaquin Rivers; 

• Bear, Marsh, Mosher, Morrison, and Ulatis Creeks; 

• Prospect and Shag Sloughs, which drain the Yolo Bypass; 

• French Camp Slough and Upper Lindsay/Cache Slough area; and 

• Manteca-Escalon, Bethany Reservoir, Antioch, and Montezuma Hills areas. 

The primary drainage in the Yolo Bypass is the Toe Drain, which drains southward to Prospect 

Slough in the legal Delta. However, depending on the level of inundation in the Yolo Bypass, 

about 20% of the incoming water may drain to the Delta by way of Shag Slough (Foe et al., 

2008). The following watershed areas drain to the Yolo Bypass upstream of Prospect and Shag 

Sloughs: 

• Cache Creek Settling Basin 

• Fremont and Sacramento Weirs 

• Knights Landing Ridge Cut 

• Putah Creek 

• Willow Slough and Willow Slough Bypass 

• Dixon Area

Putah Creek drains to the Yolo Bypass downstream of the legal Delta boundary, while the rest 

of the watershed areas drain to it upstream of the legal Delta boundary. Fremont and 

Sacramento Weirs convey floodwaters from the Sacramento and Feather Rivers, Sutter Bypass 

and their associated tributary watersheds. The Knights Landing Ridge Cut is an overflow 

channel that connects the Colusa Basin Drain to the Yolo Bypass (see Figure 6.1 and 

Figure E.2 in Appendix E). 

Several sampling efforts have taken place to characterize tributary inputs to the Delta and Yolo 

Bypass. Figure 6.2 shows the tributary methylmercury monitoring locations. Appendix L 

provides the methylmercury concentration data collected at each tributary location and 

Table 6.3 and Figure 6.3 summarize the data. 

Central Valley Water Board staff conducted monthly aqueous methylmercury sampling in the 

four major tributaries – Sacramento River, San Joaquin River, Mokelumne River, and Prospect 

Slough – from March 2000 to September 2001 (Foe, 2003). In addition, other programs 

conducted periodic aqueous methylmercury sampling on the Sacramento River between July 

2000 and June 2003 (SRWP, 2004; CMP, 2004; Stephenson et al., 2002). Monthly sampling of 

the major tributaries and periodic sampling of other tributaries by Central Valley Water Board 

staff resumed in April 2003. Of the three Sacramento River sampling locations included in the 

linkage analysis (Chapter 5) – Freeport, River Mile 44 and Greene’s Landing – Freeport is the 
most upstream location and is used to characterize loads from the Sacramento River 

watershed33 (Table 6.2). 

The Sacramento Weir did not spill to the Yolo Bypass during WY2000-2003; hence, no 

methylmercury load estimate was made for Sacramento Weir inputs. Methylmercury loads 

contributed by Fremont Weir spills were estimated using methylmercury concentration data 

collected from the Sacramento River at Colusa because field observations indicate that Fremont 

Weir spills are typically comprised of flows from the Sacramento River upstream of the Feather 

River confluence (Foe, pers. comm.). Methylmercury loads contributed by the Knights Landing 

Ridge Cut were estimated using methylmercury concentration data collected from the Colusa 

Basin Drain at Knights Landing. 

Methylmercury data were not available for several of the small watersheds and drainage areas 

that discharge to the Delta and Yolo Bypass. The average methylmercury concentration for 

Ulatis Creek was used to estimate Willow Slough/Bypass, Upper Lindsay/Cache Slough, and 

Dixon area inputs because they have similar land uses as the Ulatis Creek watershed and are 

adjacent to each other. No methylmercury load estimates were made for the other small 

drainage areas (Manteca-Escalon, Bethany Reservoir, Antioch, and Montezuma Hills areas); 

given that these areas contribute only about one third of a percent of all water inputs to the 

Delta/Yolo Bypass, methylmercury loads from these areas are not expected to be substantial. 

Regressions between methylmercury concentration and daily flow were evaluated for each 

tributary input with available flow gage records to determine whether concentrations could be 

predicted from flow (Appendix F). Only the regression for the Sacramento River was significant 

(P<0.05). The Sacramento River regression explained 12% of the variation in methylmercury 

concentrations. Lack of a relationship between methylmercury concentrations and flow at all 

sites except the Sacramento River suggests that flow is unlikely to be a useful surrogate for 

methylmercury concentrations. The relationship at Freeport may be a statistical anomaly. 

Therefore, average methylmercury concentrations were used to estimate all tributary loads. For 

tributary inputs with a monthly sampling frequency (Table 6.3), concentration data were pooled 

by month to calculate monthly average concentrations for WY2000-2003 (Table F.1 in 

Appendix F). The monthly average concentrations were multiplied by monthly average flow 

volumes (Table F.2) to estimate loads; monthly loads were summed to calculate an annual 

average methylmercury load for WY2000-2003. For all the tributaries with less frequent 

sampling, loads were estimated by multiplying average annual water volume for WY2000-2003 

(Table 6.1) by the average wet weather methylmercury concentration for each tributary input 

(Table 6.3). 

Methylmercury loads in Yolo Bypass outflows at Prospect Slough were evaluated for 

comparison to Yolo Bypass inputs and other major tributaries (e.g., the Sacramento and San 

Joaquin Rivers). Methylmercury concentration data for Shag Slough outflows were not 

available at the time the TMDL was developed. Although sampling took place on a regular 

 

33 The Delta area that drains to the 13-mile reach of the Sacramento River between Freeport (near river mile 46) and 

the I Street Bridge (the northernmost legal Delta boundary, near river mile 59) is predominantly urban and is 

encompassed by the urban load estimate described in Section 6.2.5. No attempt was made to subtract this area 

from the Sacramento River watershed load estimate. Therefore, the Sacramento River load noted in Table 6.2 

incorporates a small portion of the within-Delta urban runoff loading. 

Delta Methylmercury TMDL Report 82 April 2010 
basis at Prospect Slough in the Yolo Bypass, only six sampling events occurred when there was 

net advective outflow at the Lisbon Weir (Appendix E, Section E.2.2). Dispersive or tidal flows 

also transport loads from the Bypass below the Lisbon Weir during almost all times; however, 

the actual amount is unknown at present. Therefore, annual methylmercury loading from 

Prospect Slough was estimated by multiplying average methylmercury concentrations observed 

when the slough had net outflow (0.346 ng/l) by the annual average net advective outflow from 

the Yolo Bypass (1.0 M acre-ft/yr for WY2000-2003, see Appendix E, Section E.2.2). 

The resulting Yolo Bypass load (443 g/yr) is comparable to the sum of watershed inputs to the 

Yolo Bypass (440 g/yr). However, this load estimate probably underestimates export from the 

Bypass because, although it is based on the estimated total outflow from the Bypass, it uses 

methylmercury concentrations observed at Prospect Slough, and does not include outflows from 

Shag Slough. Recent data indicate that Shag Slough has elevated methylmercury 

concentrations (Foe et al., 2008), possibly due to its proximity to mercury-contaminated inputs 

from Cache and Putah Creeks. Even so, this uncertainty is unlikely to substantially affect the 

load estimates for WY2000-2003, a relatively dry period (Appendix E, Section E.1). For 

example, the Fremont Weir and Cache Creek Settling Basin weir, the primary tributary water 

sources to the Yolo Bypass, did not spill at all during WY2001 (see Appendix E, Figure E.4). 

Foe and others (2007) found the Yolo Bypass to be a net producer of methylmercury, when 

conveying floodwaters. Additional evaluation is needed to determine how much methylmercury 

is produced within the Yolo Bypass and how much is delivered from upstream watersheds 

during both wet and dry years. Central Valley Water Board staff recently completed a study that 

found that in situ methylmercury production within the Yolo Bypass averaged 40% of the 

methylmercury loading to the Delta from the entire Sacramento Basin (Foe et al., 2008). The 

study authors found this surprising because the Yolo Bypass is only 59,000-acres while the 

Sacramento Basin is 16,765,000-acres or 285 times larger. When there are no flood flows in 

the bypass, the wetlands and other lands in the bypass have little-to-no discharge to the Delta. 

The final results of this study and any additional studies conducted during the first phase of the 

Delta mercury control program implementation will be incorporated into TMDL calculations 

during the Delta mercury control program review at the end of the first phase of implementation. 

The Sacramento River was the primary tributary source of methylmercury (2.0 kg/yr) during 

WY2000-2003 (Table 6.2). LWA (2002) calculated an annual average methylmercury load of 

3.2 ±1.6 kg/yr for the Sacramento River at Freeport for 1980-1999 (a wetter period than the 

TMDL base period). Foe (2003) also concluded that the Sacramento River was the major 

methylmercury tributary source in all months between March 2000 and September 2001, except 

for March 2000 when the Yolo Bypass was flooded and it became the primary source of 

methylmercury. Water years 2000 through 2003 were considered normal to dry years in the 

Sacramento and San Joaquin watersheds. Therefore, tributary loads for the TMDL study period 

may underestimate long-term values. In particular, the Yolo Bypass may provide a more 

substantial methylmercury load to the Delta when flooded for prolonged periods, as in 1997 

and 1998. 

Delta Methylmercury TMDL Report 83 April 2010 
Figure 6.1: Watersheds that Drain to the Delta and Yolo Bypass. 

Delta Methylmercury TMDL Report 84 April 2010 
Figure 6.2: Tributary Aqueous Methylmercury Monitoring Locations 

Delta Methylmercury TMDL Report 85 April 2010 
Table 6.3: Methylmercury Concentrations for Tributary Inputs. 

Site (a)

# of 

Samples 

Sampling 

Begin Date

Sampling End Date 

Min. MeHg 

Conc. (ng/l) 

Ave. MeHg 

Conc. (ng/l) 

Annual Ave. 

MeHg (ng/l) (a) M

C

Large Tributaries to the Delta Cache Creek Settling Basin Outflow 8 3/1/2000 9/29/2003 0.155 0.504 0.504 Fremont Weir (Sacramento River @ Colusa) 30 7/20/2000 9/15/2003 0.041 0.105 0.097 (0.102) (b) Knights Landing Ridge Cut (Colusa Basin Drain @ Road 99E) 21 7/21/2000 9/15/2003 0.080 0.214 0.191 Mokelumne River @ I-5 23 3/28/00 9/30/03 0.011 0.153 0.166 Putah Creek @ Mace Blvd 23 3/28/2000 9/29/2003 0.053 0.197 0.180 Prospect Slough (Yolo Bypass) (c) 22 (6) 3/28/00 9/30/03 0.114 (0.142) 0.256 (0.346) 0.273 (0.346) Sacramento River @ Freeport 36 7/18/00 6/11/03 0.050 0.105 0.103 San Joaquin River @ Vernalis 31 3/28/00 4/12/04 0.093 0.156 0.160 Small Tributaries to the Delta Bear Creek @ West Lane 3 2/2/04 2/26/04 0.336 0.404 0.310 Calaveras River @ RR u/s West Lane 4 3/15/03 2/26/04 0.110 0.144 0.144 French Camp Slough d/s Airport Way 5 1/28/02 2/26/04 0.063 0.127 0.142 Marsh Creek @ Hwy 4 7 3/15/03 2/2/04 0.090 0.224 0.255 Morrison Creek @ Franklin 1 1/28/02 1/28/02 0.102 0.102 0.102 Mosher Creek @ Morada Lane (d) 1 3/15/03 3/15/03 0.028 0.028 (d) Ulatis Creek near Main Prairie Rd 6 1/28/02 2/26/04 0.004 0.172 0.240 (a) For the large tributary inputs, methylmercury concentration data were pooled by month to estimate monthly average methylmercury concentrations a

loads were summed to estimate annual average methylmercury loads for water years 2000-2003. The methylmercury concentration data are providemonthly average concentrations and flows are listed in Appendix F. The monthly average concentrations were averaged to estimate annual average included in Table 6.2. Sampling on the small tributaries and Cache Creek Settling Basin did not take place monthly, and flow gages were unavailablavailable methylmercury concentration data were averaged to estimate annual average methylmercury concentrations and loads for the Cache Cree

weather methylmercury concentration data were averaged to estimate annual average methylmercury concentrations and loads for the small tributar

(b) The average of monthly average concentrations for Sacramento River at Colusa for months when Fremont Weir spilled during WY2000-2003 (Janua

and December) is shown in parentheses. 

(c) Only six Prospect Slough MeHg sampling events took place when there was a net outflow. These sampling events are described in parentheses. M

during other times were strongly affected by tidal pumping of waters from the Sacramento River. 

(d) The one Mosher Creek sample result was combined with the Bear Creek methylmercury data to estimate methylmercury loads for both creeks. 

Delta Methylmercury TMDL Report 86 
Mokelumne River @ I-5

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

Prospect Slough (Yolo Bypass)

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

Sacramento River @ Freeport

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

San Joaquin River @ Vernalis

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

Cache Creek Settling Basin Outflow

0

0.3

0.6

0.9

1.2

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l) 

Colusa Basin Drain @ Road 99E

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

Putah Creek @ Mace Blvd.

0

0.4

0.8

1.2

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

Sacramento River @ Colusa

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

Figure 6.3a: Methylmercury Concentrations for Major Tributary Inputs 

Delta Methylmercury TMDL Report 87 April 2010 
Small Westside Tributaries

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

Ulatis Creek

M arsh Creek

Small Eastside Tributaries

0

0.2

0.4

0.6

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MeHg Conc. (ng/l)

M orrison Creek

Bear Creek

M osher Creek

Calaveras River

French Camp Sl.

Figure 6.3b: Methylmercury Concentrations for Small Tributary Inputs 

6.2.2 Within-Delta Sediment Flux 

Methylmercury flux from within-Delta sediments is estimated to contribute about 36% of the 

overall methylmercury load (Table 6.2). Methylmercury loads from bottom sediment in open 

water were estimated from flux rates measured by Gill and others (2003). Wetland flux rates 

were from Heim, Sassone and others (Heim et al., 2004; Sassone et al., 2004) and a load 

calculation method outlined by Heim and others (Heim, 2004; Heim et al., 2004). To measure 

methylmercury flux in open water habitats, Gill and others (2003) deployed benthic flux 

chambers at nine locations in the Bay-Delta region during five separate field-sampling efforts 

between May 2000 and October 2001. This study estimated a methylmercury flux rate of 

approximately 10 ng/m2

/day for open water habitat. An additional study of sediment-water 

MeHg flux within marsh and wetland habitat was conducted at two experimental ponds on 

Twitchell Island (Heim et al., 2004; Sassone et al., 2004). The west pond, which had more 

shallow water and greater coverage of emergent vegetation, had sediment-water flux rates of 

41 ng/m2

/day during June 2003, while the flux from the east pond had a flux rate of 3 ng/m2/day. 

In October 2003, the flux from both ponds decreased to 3 ng/m2

/day. Heim (2004) 

recommended that the flux rates for the west pond be used to estimate warm and cool season 

loads; the warm season was defined as March through September (214 days) and the cool 

season as October through February (151 days). 

water were estimated from flux rates measured by Gill and others (2003). Wetland flux rates 

were from Heim, Sassone and others (Heim et al., 2004; Sassone et al., 2004) and a load 

calculation method outlined by Heim and others (Heim, 2004; Heim et al., 2004). To measure 

methylmercury flux in open water habitats, Gill and others (2003) deployed benthic flux 

chambers at nine locations in the Bay-Delta region during five separate field-sampling efforts 

between May 2000 and October 2001. This study estimated a methylmercury flux rate of 

approximately 10 ng/m2

/day for open water habitat. An additional study of sediment-water 

MeHg flux within marsh and wetland habitat was conducted at two experimental ponds on 

Twitchell Island (Heim et al., 2004; Sassone et al., 2004). The west pond, which had more 

shallow water and greater coverage of emergent vegetation, had sediment-water flux rates of 

41 ng/m2

/day during June 2003, while the flux from the east pond had a flux rate of 3 ng/m2/day. 

In October 2003, the flux from both ponds decreased to 3 ng/m2

/day. Heim (2004) 

recommended that the flux rates for the west pond be used to estimate warm and cool season 

loads; the warm season was defined as March through September (214 days) and the cool 

season as October through February (151 days). 

Wetland and open water acreages were estimated using the 2006 National Wetland Inventory 

coverage for the Delta region (USFWS, 2006; Figure 6.4). Types of wetland habitat in the Delta 

and Yolo Bypass are predominantly seasonal wetlands and tidal, salt, brackish and freshwater 

marshes. The open-water, warm season wetland and cool season wetland flux rates were 

multiplied by the open water and wetland areas, respectively, to estimate daily loading. The 

daily loads were multiplied by the number of days in the warm and cool seasons and then 

summed to estimate annual loading. The loads to each Delta subarea were calculated 

(Table 6.4) to develop subarea-specific allocations (Chapter 8). The Yolo Bypass subarea has 

the greatest methylmercury loading from sediment because it has the greatest acreage of 

wetlands; the Central Delta subarea is second because it has the greatest amount of open 

water habitat. Methylmercury loading from wetland and open water sediments in each subarea 

Wetland and open water acreages were estimated using the 2006 National Wetland Inventory 

coverage for the Delta region (USFWS, 2006; Figure 6.4). Types of wetland habitat in the Delta 

and Yolo Bypass are predominantly seasonal wetlands and tidal, salt, brackish and freshwater 

marshes. The open-water, warm season wetland and cool season wetland flux rates were 

multiplied by the open water and wetland areas, respectively, to estimate daily loading. The 

daily loads were multiplied by the number of days in the warm and cool seasons and then 

summed to estimate annual loading. The loads to each Delta subarea were calculated 

(Table 6.4) to develop subarea-specific allocations (Chapter 8). The Yolo Bypass subarea has 

the greatest methylmercury loading from sediment because it has the greatest acreage of 

wetlands; the Central Delta subarea is second because it has the greatest amount of open 

water habitat. Methylmercury loading from wetland and open water sediments in each subarea 

Delta Methylmercury TMDL Report 88 April 2010 
was summed so that the Delta-wide methylmercury loading from sediments could be compared 

with other sources in Table 6.2. 

Using the Twitchell Island west pond summer flux rates, methylmercury loading from wetlands 

in the Delta/Yolo Bypass accounts for about 19% of all methylmercury to the Delta during the 

relatively dry period of WY2000-2003. However, if the east pond data had been used, 

methylmercury loading from wetlands would account for only about 3% of all methylmercury to 

the Delta. In addition, research completed since the February 2008 draft TMDL Report 

(Sassone et al, 2008; Stephenson et al., 2008) indicates that the Twitchell Island west pond flux 

rates are lower than initially estimated from the preliminary monitoring results, and that the 

Twitchell Island ponds are not characteristic of all wetlands in the Delta region, in part because 

they receive continual inputs of water (compared to seasonal wetlands). This illustrates the 

need for better characterization of wetlands throughout the Delta and Yolo Bypass, particularly 

of the seasonality of their discharges. Nonetheless, research elsewhere in California and the 

United States has found that wetlands are sites of efficient methylmercury production (Slotton et 

al., 2003; Heim et al., 2003; St. Louis et al., 1994, 1996; Gilmour et al., 1998), so much so that 

one of the best predictors of methylmercury concentrations in water and in biota is the amount 

of wetland present in upstream watersheds (Krabbenhoft et al., 1999; Wiener et al., 2003b). 

Until additional research has been conducted in the Delta and Yolo Bypass, the Twitchell Island 

west pond summer flux rates will be used to estimate methylmercury loading from wetlands for 

the TMDL. As described in the draft Basin Plan Amendment staff report, staff recommends that 

a control program review take place after additional Delta-specific studies are completed, during 

which the TMDL source analysis can be updated. 

Space intentionally left blank. 

Delta Methylmercury TMDL Report 89 April 2010 
Figure 6.4: Delta and Yolo Bypass Wetlands and Open Water Habitat. Wetland areas include seasonal 

wetlands and brackish and freshwater marshes. (Wetland and open water acreage: USFWS, 2006.) 

Delta Methylmercury TMDL Report 90 April 2010 
Table 6.4: Methylmercury Loading from Wetland and Open Water Habitats in Each Delta Subarea. (a)

Central 

Delta 

Cosumnes / 

Mokelumne 

River 

Marsh

Creek

Sacramento 

River 

San 

Joaquin 

 River 

West 

Delta 

Yolo BypassNorth (d) Y

Open Water Habitats 

Open Water (acres): 25,141 271 12.0 9,483 3,246 13,118 1,281 

% of Total Water Area: 43% 0.47% 0.02% 16% 5.6% 23% 2.2% 

Open Water (m2): 101,743,759 1,096,558 48,501 38,375,389 13,136,719 53,088,806 5,185,613 

Daily Open Water MeHg Load (g/day) (b): 1.02 0.0110 0.0005 0.38 0.13 0.53 0.052 

Annual Open Water MeHg Load (g/year): 371 4.0 0.18 140 48 194 19 

Wetland Habitats (c)

Wetland Area (acres): 5,594 803 9.2 2,538 1,170 3,609 1,577 

% of Total Wetland Area: 21% 3.0% 0.03% 9.6% 4.4% 14% 5.9% 

Wetland Area (m2): 22,636,361 3,250,048 37,399 10,272,237 4,735,497 14,605,419 6,382,048 

Warm Season MeHg Daily Load (g/day): 0.92 0.13 0.0015 0.42 0.19 0.59 0.26 

Cool Season MeHg Daily Load (g/day): 0.068 0.010 0.00011 0.031 0.014 0.044 0.019 

Annual Wetland MeHg Load (g/year): 207 29.7 0.34 94 43 134 58 

Annual MeHg Load (grams/year): 578 34 0.52 234 91 327 77 

(a) Wetland and open water habitat acreages were obtained from the National Wetland Inventory (USFWS, 2006). (b) The daily open water MeHg load for each Delta subarea was estimated by multiplying its open water area by the open water sediment flux rate, 10 ng/m2

rate was developed by Gill and others using benthic flux chambers (Gill et al., 2003). 

(c) The daily warm season and cool season wetland MeHg loads for each Delta subarea were estimated by multiplying the open water area by the warm and 

41 ng/m2/day and 3 ng/m2/day. The warm and cool season wetland flux rates were developed by Heim and others (2004) using direct measurement of and outflows from test wetlands on Twitchell Island in the west Delta. The warm season for the wetland flux rate is defined approximately as March throucool season is defined approximately as October through February (151 days) (Heim, 2004). The annual load was estimated by multiplying the number o

seasons by the daily warm and cool season loads, respectively, and summing the resulting seasonal loads. 

(d) The Yolo Bypass-North subarea includes wetland and open water areas in the Yolo Bypass north of the legal Delta boundary. 

Delta Methylmercury TMDL Report 91 
6.2.3 Municipal & Industrial Sources 

Information about NPDES-permitted municipal and industrial dischargers in the Delta and Yolo 

Bypass was obtained from the State Water Resources Control Board’s Surface Water 

Information (SWIM) database and from the Central Valley Water Board’s discharger project files 

and permits. During the TMDL period, WY2000-2003, there were 23 NPDES-permitted 

municipal and industrial dischargers in the Delta and Yolo Bypass (Figure 6.5, Table 6.5). 

These facility discharges accounted for about 4% (205 g/yr) of the annual methylmercury 

loading to the Delta/Yolo Bypass during the WY2000-2003 period (Table 6.2). Since then, 

several facilities have ceased discharging to surface waters and others have begun discharging. 

The following paragraphs describe past and present (as of January 2010) discharges, available 

effluent methylmercury data, and load calculation methods. 

As described in Sections 6.2.1 and 6.3.1, the WY2000-2003 period encompasses the 

methylmercury concentration data available for the major Delta tributary inputs and exports at 

the time TMDL development took place. However, only one NPDES-permitted discharger 

collected effluent methylmercury data during this period. Between December 2000 and June 

2003, the Sacramento Regional County Sanitation District (SRCSD) collected 60 samples to 

characterize its effluent methylmercury levels. In February and March 2004, Central Valley 

Water Board staff conducted two sampling events at four municipal wastewater treatment plants 

(WWTPs) to determine whether the SRCSD data are representative of other municipal 

wastewater treatment plants’ effluent methylmercury levels. The 2004 sampling results 

indicated that the methylmercury data from the SRCSD facility may not be representative of 

other facilities in the Delta region. Therefore, the Central Valley Water Board issued a 

California Water Code Section 13267 order in July 2004 requiring municipal WWTPs and other 

dischargers located in the Delta and in the Delta’s tributary watersheds downstream of major 

dams to monitor and characterize their effluent. 

Table 6.5 summarizes the results of available methylmercury data for facility discharges in the 

Delta and Yolo Bypass. Table G.3 in Appendix G provides a summary of the methylmercury 

data generated by NPDES facility sampling efforts throughout the Delta region. A detailed 

review of the data is provided in the Central Valley Water Board staff report, “A Review of 

Methylmercury and Inorganic Mercury Discharges from NPDES Facilities in California’s Central 

Valley” (Bosworth et al., 2010), along with a copy of the letter and a list of facilities that received 

the Section 13267 order and a summary of all available methylmercury data for facility 

discharges to the Delta and its tributary watersheds. Appendix L of this report provides the 

available data for facilities within the legal Delta boundary and Yolo Bypass. 

Delta Methylmercury TMDL Report 92 April 2010 
Mountain House CSD WWTP

Lincoln Center Groundwater

Treatment Facility 

Figure 6.5: NPDES Facilities that Discharge to the Statutory Delta and Yolo Bypass. 

Delta Methylmercury TMDL Report 93 April 2010 
Table 6.5: Summary of Unfiltered Methylmercury Concentration Data for Effluent from NPDES-permitted Facilities That Di

Yolo Bypass North of the Delta during the WY2000-2003 Period and Later.

Facility Name (a)

Discharged during 

 WY2000-2003 

Discharged as of 

 February 2010 NPDES # Facility Type Delta Subarea # of MeHg Sampling Events Average MeHg Conc. (ng/l) (b) MeHg Conc. Range (ng/l) # of Non- detect Results MeHg Sampling Period 

Brentwood WWTP X X CA0082660 Mun. WWTP Marsh Ck 13 0.02 (ND) (b) All ND (b) 13 8/04-8/05 Davis WWTP (Discharge 001) (g)

X X CA0079049 Mun. WWTP Yolo Bypass 7 0.55 0.305-1.04 0 8/04-1/05, 7/05 

Davis WWTP (Discharge 002) (g)

X X CA0079049 Mun. WWTP Yolo Bypass 5 0.61 0.247-1.44 0 2/05-6/05 

Deuel Vocational Institute WWTP (e)

X X CA0078093 Mun. WWTP San Joaquin 3 0.02 (ND) All ND 3 1/05-6/05 

Discovery Bay WWTP X X CA0078590 Mun. WWTP Central 12 0.19 ND-2.03 7 8/04-7/05 GWF Power Systems X X CA0082309 Power West 4 0.03 (ND) All ND 4 8/04-5/05 Lincoln Center Groundwater Treatment Facility 

X X 

CA0084255 Groundwater Treatment Central (i) (i) (i) (i) (i) 

Lodi White Slough WWTP (f)

X X CA0079243 Mun. WWTP Central 10 0.15 ND-1.24 3 9/04-6/05 

Manteca WWTP X X CA0081558

Mun. WWTP San Joaquin 11 0.22 0.037-0.356 0 9/04-7/05 

Mirant Delta LLC Contra Costa Power Plant (Outfall 1) 

X X 

CA0004863 Power West 12 0.07 0.020-0.121 0 2/04-5/05 

Mirant Delta LLC Contra Costa Power Plant (Outfall 2) 

X X 

CA0004863 Power West 10 0.09 0.042-0.15 0 2/04-3/05 

Mountain House CSD WWTP X CA0084271 Mun. WWTP San Joaquin 21 0.05 (ND) ND (0.05) - 0.05 17 8/07-5/09 Oakwood Lake Subdivision Mining Reclamation (d)

X X CA0082783 Lake Dewatering San Joaquin 2 0.03 ND-0.043 1 8/04- 11/04 

Rio Vista WWTP X X CA0079588

Mun. WWTP Sacramento 4 0.16 0.035-0.522 0 8/04-4/05 

Delta Methylmercury TMDL Report 94 
Delta Methylmercury TMDL Report 95 

Table 6.5: Summary of Unfiltered Methylmercury Concentration Data for Effluent from NPDES-permitted Facilities That Di

Yolo Bypass North of the Delta during the WY2000-2003 Period and Later.

Facility Name (a)

Discharged during 

 WY2000-2003 

Discharged as of 

 February 2010 NPDES # Facility Type Delta Subarea # of MeHg Sampling Events Average MeHg Conc. (ng/l) (b) MeHg Conc. Range (ng/l) # of Non- detect Results MeHg Sampling Period 

Rio Vista Trilogy X CA0083771 Mun. WWTP Sacramento (i) (i) (i) (i) (i) Rio Vista Northwest WWTP (i)

X CA0083771 Mun. WWTP Sacramento (i) (i) (i) (i) (i) 

Sacramento Combined WWTP X X CA0079111 Mun. WWTP Sacramento 10 0.536 0.299-0.820 0 12/04- 3/06 San Joaquin County Service Area 31 Flag City WWTP 

X CA0082848 Mun. WWTP Central 3 0.08 ND-0.152 1 1/05- 10/05 

SRCSD Sacramento River WWTP X X CA0077682 Mun. WWTP Sacramento 60 0.72 0.118- 1.64 (h) 0 12/00- 6/03 SRCSD Walnut Grove WWTP (e)

X CA0078794 Mun. WWTP Sacramento 2 2.2 0.949-3.36 0 1/05-4/05 

State of California Central Heating and Cooling Plant 

X 

CA0078581 Heating / Cooling Sacramento 4 0.01 ND-0.029 3 8/04-6/05 

Stockton WWTP X X CA0079138 Mun. WWTP San Joaquin 12 0.94 ND-2.09 1 8/04-7/05 Tracy WWTP X X CA0079154 Mun. WWTP San Joaquin 13 0.14 ND-0.422 1 8/04-8/05 West Sacramento WWTP 

X CA0079171 Mun. WWTP Sacramento 12 0.05 ND-0.085 1 8/04-7/05 

Woodland WWTP X X CA0077950 Mun. WWTP Yolo Bypass 12 0.03 ND-0.059 2 8/04-7/05 
Table 6.5 Footnotes:

(a) No methylmercury or discharge volume data are available for Metropolitan Stevedore (CA0084174), a marine bulk commodity 

terminal in the Central Delta subarea. 

(b) ND: nondetect (below method detection limit). Analytical method detection limits were 0.025 ng/l or less, except for the 

Mountain House CSD WWTP data, which had a detection limit of 0.05 ng/l. One half the detection limit was used for nondetect 

values to calculate the average methylmercury concentrations and loads, except when a facility reported all data as equal to or

less than the nondetect limit, in which case the detection limit was used to calculate loads. 

(c) Based on the comparison of the available intake and outfall methylmercury data (Table G.4 in Appendix G), power and 

heating/cooling facilities that use ambient water for cooling water do not appear to act as a source of new methylmercury to the 

Delta. This assumption will be re-evaluated as additional information becomes available. 

(d) The Oakwood Lake Subdivision Mining Reclamation was formerly known as the Manteca Aggregate Sand Plant. 

(e) Results for the following facilities and sample dates were not incorporated in the summary calculations due to sample 

preservation hold times exceeding USEPA recommendations: Deuel Vocational Institute WWTP (26 October 2004, <MDL) and 

SRCSD Walnut Grove WWTP (29 December 2004, 0.759 ng/l). 

(f) Lodi White Slough WWTP sampled effluent when discharging to land and to surface water. Only samples collected when the 

WWTP discharged to surface water (September 2004 through June 2005) were used in the summary. Effluent that was 

reclaimed in August 2004 and July 2005 had methylmercury concentrations of 0.054 ng/l and <0.020, respectively. 

(g) The City of Davis WWTP (CA0079049) has two seasonal discharge locations; wastewater is discharged from Discharge 001 to 

the Willow Slough Bypass upstream of the Yolo Bypass and from Discharge 002 to the Conaway Ranch Toe Drain in the Yolo 

Bypass. The Discharge 001 methylmercury load is based on effluent volumes for October 2004 through January 2005 plus 

July 2005 through September 2005. The Discharge 002 methylmercury load is based on effluent volumes for February 2005 

through June 2005. 

(h) The SRCSD Sacramento River WWTP (CA0077682) methylmercury concentration data was collected between December 

2000 and June 2003. Two data points failed SRCSD’s Quality Assurance review (7/13/2001: 2.93 ng/l, 6/18/2006: 0.08 ng/l); 

these data are not included in the TMDL calculations. 

(i) No effluent methylmercury concentration data were available for the City of Rio Vista’s Trilogy WWTP and Northwest WWTPs 

or the Lincoln Center Groundwater Treatment Facility. As explained in detail in the text, their effluent methylmercury loads 

were estimated by using effluent methylmercury concentration data available for other facilities with similar treatment 

processes. 

6.2.3.1 Municipal WWTPs 

Fifteen municipal wastewater treatment plants discharged the Delta/Yolo Bypass during 

WY2000-2003. The average annual methylmercury load for SRCSD’s Sacramento River 

WWTP was calculated using the average effluent methylmercury concentrations observed 

between December 2000 and June 2003 and the average annual discharge volume for 

WY2001-2003 (October 2000 through September 2003). Average annual methylmercury loads 

were calculated for all other municipal WWTPs, except as noted in the following paragraphs, 

using the average effluent methylmercury concentrations based on available data collected 

between August 2004 and October 2005 and the annual discharge volume for WY2005 

(October 2004 through September 2005). Facility-specific average effluent methylmercury 

concentrations ranged from less than 0.02 ng/l (Brentwood and Deuel Vocational Institute 

WWTPS) to 2.2 ng/l (SRCSD Walnut Grove WWTP). 

Staff compiled and evaluated NPDES municipal WWTP effluent methylmercury data collected 

during the Section 13267 monitoring period, 2004-2005, as well as other available data for 

WWTPs in and upstream of the Delta, in a separate report: A Review of Methylmercury and 

Inorganic Mercury Discharges from NPDES Facilities in California’s Central Valley

(Bosworth et al., 2010). The effluent data for 67 municipal WWTPs in the Central Valley 

indicate that: 

• 14 facilities had average effluent methylmercury levels that approached or were less than 

analytical method detection limits (e.g., less than 0.03 ng/l) and 24 facilities had effluent 

Delta Methylmercury TMDL Report 96 April 2010 
methylmercury levels equal to or less than the proposed implementation goal (0.06 ng/l) 

for ambient water. This indicates that it is possible for WWTPs to have effluent 

methylmercury concentrations lower than the proposed implementation goal. 

• 19 facilities had effluent exceeding 0.2 ng/l methylmercury and 7 facilities had effluent 

exceeding 1 ng/l methylmercury. This demonstrates that methylmercury in effluent is 

variable between WWTPs. 

• Eleven of the 12 facilities with the highest effluent methylmercury made use of some type 

of pond system for treatment; none of the facilities with effluent methylmercury less than 

0.2 ng/l made use of pond systems. This indicates that the type of treatment process may 

affect effluent methylmercury levels. 

• One municipal WWTP in the Delta, SRCSD’s Sacramento River WWTP, had effluent 

methylmercury data for 2001-2007; the data illustrate a marked decrease in effluent 

methylmercury and total mercury concentrations with time. The decline indicates that it is 

possible for a given WWTP’s effluent methylmercury to decrease. During the April 2008 

Board hearing meeting for the Delta mercury control program, the SRCSD District 

Engineer testified that implementation of the Be Mercury Free Program to reduce 

inorganic mercury sources to SRCSD’s WWTP resulted in reductions in both inorganic 

mercury and methylmercury discharges from the WWTP. 

The variability in the methylmercury concentrations observed in effluent from different municipal 

WWTPs in the Delta and its upstream watersheds is comparable to WWTP effluent 

concentrations observed elsewhere. Sampling at the San Jose/Santa Clara Water Pollution 

Control Plant in California indicated an average effluent methylmercury concentration of 

0.04 ng/l (SJ/SC, 2007). A study that evaluated methylmercury concentrations in three 

domestic sewage treatment plants at the City of Winnipeg, Canada, found average effluent 

methylmercury concentrations to be very low at two facilities (0.13 to 0.56 ng/l, no seasonal 

trend) and higher at a third (greater than 2 ng/l, with highest concentrations in the summer) 

(Bodaly et al., 1998). A separate study that evaluated seasonal patterns in sewers and 

wastewater unit processes in the Onondaga County Metropolitan Wastewater Treatment Plant 

in Syracuse, New York, observed a mean methylmercury concentration (± standard deviation) 

of 1.63 ± 1.19 and 1.43 ± 0.67 ng/l in warm and cool months, respectively; a peak of 3.70 ng/l 

was measured in May (McAlear, 1996). Additional information about facilities elsewhere in 

California and the United States is provided in “A Review of Methylmercury and Inorganic 

Mercury Discharges from NPDES Facilities in California’s Central Valley”

(Bosworth et al., 2010). 

Some type of seasonal or other treatment-related variability was observed in effluent 

methylmercury concentrations at several of the municipal WWTPS in the Delta and its tributary 

watersheds (Bosworth et al., 2010). Identifying the reasons why some facilities discharge 

effluent with higher methylmercury concentrations than others, and why some facilities have 

seasonal or other treatment-related variability in their methylmercury discharges, could be 

critical components to the development of methylmercury controls.34 

 

34 In addition, seasonal increases in effluent methylmercury loading from some facilities could result in a greater 

influence on local water bodies, especially during the dry season. For example, SRCSD Sacramento River WWTP 

(the largest permitted facility discharge in the Central Valley) has an annual effluent methylmercury load (161 g/yr, 

Delta Methylmercury TMDL Report 97 April 2010 
As noted earlier, several municipal WWTPs in the Delta/Yolo Bypass have ceased discharging 

to surface waters, others have begun discharging, and one has had substantial modifications to 

its treatment processes since WY2003. In summary: 

• The San Joaquin County Service Area 31 Flag City WWTP, Walnut Grove WWTP, West 

Sacramento WWTP, and Rio Vista Trilogy WWTP have ceased discharging to surface 

water; 

• The Mountain House WWTP and Northwest WWTP began discharging to surface water; 

• The Stockton WWTP has had substantial treatment upgrades. 

The San Joaquin County Service Area 31 Flag City WWTP was discharging to surface water 

during the WY2000-2003 period. As a result, its effluent methylmercury load is included in the 

Table 6.2 summary. However, the discharger recently completed the construction of a pump 

station and dual forcemain project that allows for discharge of the Flag City wastewater to the 

City of Lodi White Slough WWTP. As of 10 April 2008, all wastewater flows from the Flag City 

area are being directed to the Lodi WWTP, and the Flag City WWTP’s discharge to surface 

waters has ceased. Chapter 8 addresses this change in the allocation calculation for the Lodi 

WWTP. 

Because the West Sacramento and Walnut Grove WWTPs discharged to surface waters during 

the TMDL period, WY2000-2003, their effluent methylmercury loads shown in Table 6.5 are 

included in the Table 6.2 load summary. However, as part of regionalization efforts, SRCSD’s 

Sacramento River WWTP now receives influent that had been treated by the West Sacramento 

and Walnut Grove WWTPs. Chapter 8 addresses this regionalization in the allocation 

calculation for the Sacramento River WWTP. 

The Rio Vista Trilogy WWTP had an annual average dry weather flow of 0.10 mgd. Trilogy 

discharged treated wastewater to land during irrigation months (May through October) and to an 

unnamed ephemeral stream during non-irrigation months. The Trilogy WWTP was equipped 

with flow equalization, primary clarification, trickling filtration, secondary clarification, chemical 

addition, tertiary filtration, chlorine disinfection, and emergency storage. Discharge 

methylmercury data were not available for the Trilogy WWTP. Table 23 in “A Review of 

Methylmercury and Inorganic Mercury Discharges from NPDES Facilities in California’s Central 

Valley” (Bosworth et al., 2010) indicated that municipal WWTPs that employed filtration and 

chlorination/dechlorination had average and median effluent methylmercury concentrations of 

0.105 and 0.056 ng/l, respectively, based on 134 samples from 17 facilities. Table 26 in 

Bosworth and others’ 2010 report indicates that the one facility that also had a trickling filter had 

 

see Table 6.5) that averages about 8% of its receiving water load (2,026 g/yr, Sacramento River at Freeport, see 

Table 6.2). Between December 2000 and September 2003 (the TMDL Period), SRCSD daily effluent loads during 

the wet seasons (e.g., December to April) ranged between 1 and 7% of river loads, and daily effluent volumes 

averaged about 2% of river volume (Bosworth et al., 2008). However, during the dry season, SRCSD daily effluent 

loads ranged between about 10 and 35% of river loads while effluent volume remained about 2% of river volume. 

Currently, little is known about the seasonal exposure regime controlling methylmercury concentrations in aquatic 

biota. Therefore, this TMDL is based on annual average source loads to weight all seasons equally. However, 

studies are planned to better determine the seasonal exposure regime when most of the methylmercury is 

sequestered in the aquatic food chain; results from these studies may lead to future revisions in the TMDL. 

Seasonal discharge information is not yet available for most methylmercury sources to the Delta, but would be 

required by the source control and characterization studies proposed by the draft implementation plan described in 

Chapter 4 of the Proposed Basin Plan Amendment draft staff report. 

Delta Methylmercury TMDL Report 98 April 2010 
an average and median of 0.058 and 0.044 ng/l, respectively. To estimate Trilogy WWTP wet 

season effluent methylmercury loads discharged to the Sacramento River during WY2000-2003, 

0.06 ng/l was multiplied by 0.1 mgd and 181 days to obtain an annual load estimate of 

0.0041 g/year. 

In 2007 the Trilogy WWTP was closed and the Northwest WWTP began to discharge in its 

place. The Central Valley Water Board Order No. R5-2004-0092 considers the closure of the 

Trilogy WWTP coinciding with the start-up of the Northwest WWTP as a change in treatment 

process and location rather than as a new treatment plant. The Northwest WWTP is equipped 

with extended aeration activated sludge biological treatment with nitrogen removal (nitrification 

and denitrification), ultrafiltration (i.e., membrane filtration), and ultraviolet (UV) disinfection. 

The new Northwest WWTP (1) makes use of UV disinfection in lieu of chlorination and 

dechlorination to prevent the formation of disinfection byproducts (trihalomethanes) and reduce 

the salt concentration of the effluent; (2) discharges directly to the Sacramento River in lieu of 

continued discharge to the unnamed tributary stream to prevent elevated salts from adversely 

affecting local agriculture, and (3) eliminates continued discharge to the golf course irrigation 

reservoir and irrigation of the golf course to prevent groundwater impacts. 

The Northwest WWTP has an average dry weather flow start-up capacity of 1 mgd but no 

effluent methylmercury data have been collected yet. Table 23 in “A Review of Methylmercury 

and Inorganic Mercury Discharges from NPDES Facilities in California’s Central Valley”

(Bosworth et al., 2010) indicated that WWTPs that employed nitrification/denitrification, filtration 

and UV disinfection had effluent methylmercury concentrations that ranged from nondetect to 

0.078 ng/l and average and median effluent methylmercury concentrations of 0.029 and 0.020 

ng/l, respectively, based on three facilities and 21 samples, 11 of which had methylmercury 

concentrations less than the method detection limit. In the absence of monitoring data, it may 

not be reasonable to estimate its effluent load or calculate an allocation for the Northwest 

WWTP based on a concentration that is less that the current calibration standard for 

methylmercury analysis (0.05 ng/l). As a result, the effluent methylmercury load was estimated 

using a concentration of 0.05 ng/l and discharge volume of 1 mgd to obtain an annual load of 

0.069 g/year. Because the Northwest WWTP was not discharging in WY2000-2003, its load is 

not included in Table 6.2. However, because it will continue to discharge for the foreseeable 

future, it is included in the allocation calculations described in Chapter 8. Because it is likely 

that the estimated effluent load for the Northwest WWTP may be an overestimate, given effluent 

methylmercury concentrations observed at WWTPs that employ similar treatment processes, its 

corresponding allocation may include a margin of safety. As described in the draft Basin Plan 

Amendment staff report, staff recommends that a control program review take place after 

additional Delta-specific studies are completed, during which the Northwest WWTP discharge 

load estimate and allocation can be updated if needed. 

The Mountain House Community Services District (CSD) WWTP was not discharging to surface 

water prior to March 2007 and therefore was not identified in the source analysis for the TMDL 

period, WY2000-2003. The Mountain House CSD WWTP now discharges to Old River within 

the San Joaquin River subarea. Because it is now discharging and has submitted effluent 

methylmercury concentration data for its discharge (see Appendix L), staff estimated its average 

annual effluent methylmercury load and calculated an allocation for its discharge. Between 

August 2007 and May 2009, 21 monthly effluent samples were analyzed for methylmercury. 

Delta Methylmercury TMDL Report 99 April 2010 
Four results were reported as equal to the detection limit (0.05 ng/l) and 17 results were 

reported as “ND” (nondetect) with a method detection limit of 0.05 ng/l. Its annual average 

discharge load shown in Table 6.5 (0.031 g/yr) was calculated using a methylmercury 

concentration of 0.05 ng/l and its Phase 1 average dry weather design capacity of 0.45 mgd. 

Because the Mountain House CSD WWTP was not discharging in WY2000-2003, its load is not 

included in the Table 6.2 summary. However, because it will continue to discharge for the 

foreseeable future, it is included in the allocation calculations described in Chapter 8. 

The City of Sacramento owns and operates a combined sewer system (CSS) that serves about 

eleven thousand acres. The CSS conveys up to 60 mgd of domestic and industrial wastewater 

and storm runoff to the SRCSD’s Sacramento River WWTP. The City of Sacramento operates 

its Combined Wastewater Treatment Plant (CA0079111) only when combined wastewater/storm 

flows exceed 60 mgd (Table G.2 in Appendix G). The Combined WWTP provides primary 

treatment with disinfection. If flows exceed total treatment and storage capacity, discharges 

may occur from Pioneer Reservoir; these discharges receive partial settleable solids and 

floatables removal, in a flow-through process, without disinfection. During extreme high flow 

conditions, discharges of untreated combined wastewater may occur at Sump 2. Discharges 

are predominantly urban storm runoff. At the time of the February 2008 draft report, no 

methylmercury data were available for the Combined WWTP or untreated CSS discharges. 

Hence, the average methylmercury concentration in wet weather urban runoff (0.241 ng/l, see 

Section 6.2.5) and average annual discharge volume (467 million gallons/year, see Table G.2b) 

were used to estimate a CSS methylmercury load of 0.43 g/yr. Since then, the City of 

Sacramento submitted methylmercury data for three samples collected from Combined WWTP 

discharges (0.295, 0.757 and 0.499 ng/l) and seven samples from Pioneer Reservoir discharges 

(0.299, 0.368, 0.457, 0.506, 0.666, 0.694 and 0.82 ng/l) between December 2004 and March 

2006 (see Appendix L). Because the average methylmercury concentration of the Pioneer 

Reservoir and Combined WWTP discharges were not significantly different, the average 

concentration of all the samples (0.536 ng/l) was used with the average annual discharge 

volume (467 million gallons/year) to obtain an updated load estimate (0.95 g/yr). 

Upgrades to the City of Stockton WWTP completed in September 2006 to meet new ammonia 

effluent limits and Title 22 (or equivalent) tertiary requirements appear to have led to reductions 

in total mercury and methylmercury as well as ammonia. Before the upgrades, the City of 

Stockton WWTP provided advanced secondary treatment including high-rate trickling filters and 

secondary clarifiers, followed by unlined facultative oxidation ponds, dissolved air flotation, 

mixed-media filters, and chlorination/dechlorination facilities. The September 2006 upgrade 

included the addition of two nitrifying biotowers and engineered wetlands to remove ammonia 

from the waste stream. The City of Stockton WWTP was also upgraded to meet Title 22 tertiary 

requirements, which included new tertiary filters and new facilities to provide coagulation, 

flocculation, and sedimentation prior to filtration. A comparison of WWTP effluent ammonia, 

inorganic mercury and methylmercury data collected before (August 2004-July 2005) and after 

(January-July 2009) the treatment plant upgrade indicates that since the WWTP was upgraded, 

average effluent ammonia concentrations decreased by 95%, and average inorganic mercury 

concentrations decreased 83% (Figure 6.6). Methylmercury effluent concentrations decreased 

by 91% (0.08 ng/l average, seven monthly samples) after the plant upgrade. Note, it is not 

known if the treatment plant upgrades are responsible for the mercury and methylmercury 

reductions, or if the reductions are a result of other operational or physical changes. Additional 

Delta Methylmercury TMDL Report 100 April 2010 
sampling may be needed to determine the cause of the decrease. In addition, methylmercury 

results for only seven monthly effluent samples have been submitted since the upgrades were 

completed. As more data are collected, Board staff will work with City of Stockton staff to 

evaluate whether the above trends are representative of current conditions. 

Although more recent effluent data are available for the Stockton WWTP discharges, its 

average annual methylmercury load shown in Table 6.5 was calculated using the average 

effluent methylmercury concentrations observed between August 2004 and July 2005 (the 

Section 13267 monitoring period) because this data set is more representative of conditions 

during the TMDL period, WY2000-2003. This is consistent with the method used to calculate 

the SRCSD Sacramento River WWTP, described at the beginning of this section. 

Space intentionally left blank. 

Delta Methylmercury TMDL Report 101 April 2010 
A. Effluent Methylmercury and Ammonia Concentrations Before and After Treatment Plant Upgrades

0.043 0.075

0.155 0.068 0.11 0.049 0.073

0

5

10

15

20

25

30

Sample Month

Effluent NH3 Concentration (mg/l)

0.0

0.5

1.0

1.5

2.0

2.5

Effluent MeHg Concentration (ng/l)

NH3 - August 2004-July 2005

NH3 - November 2008-July 2009

MeHg - August 2004-July 2005, Before Upgrades

MeHg - Jan-July 2009, After Upgrades

Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec

NH4 and MeHg were not analyzed

in June-Sept 2008.

B. Effluent Total Mercury Concentrations Before and After Treatment Plant Upgrades

0.9 1.1 1.1

0.7

1.0

0.6 0.8

0

2

4

6

8

10

12

Sample Month

Effluent Total Hg Concentration (ng/l)

August 2004-July 2005, Before Upgrades

Jan-July 2009, After Upgrades

Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec

Figure 6.6: City of Stockton WWTP Effluent Ammonia, Methylmercury, and Total Mercury Concentration 

Data Collected Before and After WWTP Upgrades 

Delta Methylmercury TMDL Report 102 April 2010 
6.2.3.2 Other Facilities 

The Oakwood Lake Subdivision Mining Reclamation (formerly known as the Manteca Aggregate 

Sand Plant) allows flood-control pumping from Oakwood Lake, a former excavation pit filled 

primarily by groundwater, to the San Joaquin River. The results from discharge sampling in 

August and November 2004, nondetect (<0.02 ng/l) and 0.043 ng/l respectively, are comparable 

to groundwater treatment plant discharges in the Delta’s tributary watersheds (refer to Table G.3 

in Appendix G) and are substantially lower than the monthly average methylmercury 

concentrations observed in the San Joaquin River at Vernalis between August and December 

(0.102 to 0.167; refer to Table F.1 in Appendix F). Average annual methylmercury loading from 

Oakwood Lake was estimated using a methylmercury concentration of 0.03 ng/l and the 

average annual discharge volume. 

The Lincoln Center Environmental Remediation Trust owns and operates a ground water 

extraction and treatment system in Stockton that discharges treated groundwater to 

Fourteenmile Slough in the Central Delta subarea. The Lincoln Center Groundwater Treatment 

Facility removes volatile organic compounds, petroleum products and lead from ground water, 

and to treat residual fluids generated during the continuing investigation, remediation, and 

monitoring activities at the site. Discharge methylmercury data are not available for the facility. 

The groundwater treatment facility discharges monitored elsewhere to date have average 

methylmercury concentrations below current method detection limits (< 0.03 ng/l; 

Bosworth et al., 2010). Consequently, the discharge methylmercury load for the Lincoln Center 

Facility shown in Table 6.5 (0.010 g/yr) was estimated using a methylmercury concentration of 

0.03 ng/l and the facility’s average discharge volume of 0.25 mgd. 

Three of the facilities in the Delta are power or heating/cooling facilities: GWF Power Systems, 

Mirant Delta LLC Contra Costa Power Plant, and the State of California Central Heating/Cooling 

Plant. Two of these facilities use ambient water for cooling water. Based on the comparison of 

the available intake and outfall methylmercury data (Table G.4 in Appendix G and 

Bosworth et al., 2010), such facilities do not appear to act as a source of new methylmercury to 

the Delta. This assumption will be re-evaluated as additional information becomes available 

(see Section 7.1.2). GWF Power Systems (CA0082309) acquires its intake water from sources 

other than ambient surface water; adequate data were available to estimate the methylmercury 

load in its discharge. 

The State of California Central Heating/Cooling Plant no longer requires a NPDES permit for the 

discharge of cooling water to the Sacramento River because the California Department of 

General Services (DGS) recently constructed cooling towers and a thermal energy storage tank. 

Consequently, DGS ceased the discharge to the Sacramento River in August 2009. Although 

the plant is listed in Table 6.5 because it discharged during the WY2000-2003 period, it is not 

given an allocation in Chapter 8 because the plant no longer discharges. 

The Metropolitan Stevedore Company operates a marine bulk commodity terminal on leased 

land at the Port of Stockton. Storm water runoff, dust suppression water, and wash down water 

from bulk materials handling operations collect in a primary retention basin and some other low 

areas onsite, and evaporate or percolate into groundwater. Discharges may occur during 

intense storm events or when annual accumulated rainfall far exceeds the average for a given 

Delta Methylmercury TMDL Report 103 April 2010 
year. Methylmercury concentrations and loads in non-storm water discharges will be evaluated 

once the Metropolitan Stevedore Company completes methylmercury monitoring. 

6.2.4 Agricultural Return Flows 

More than half a million acres of the Delta islands are under agricultural production (Figure 6.7). 

Water seeps and is diverted onto the islands for irrigation from the surrounding river channels. 

The unused water is returned to Delta waterways via a series of main drains. Many of the 

islands are predominately peat, a substance that Gill and others (2003) and Heim and others 

(2003) have shown to be a good substrate for methylmercury production. Water samples 

collected from five Delta Island main drains in June and July 2000 suggest that the agricultural 

islands are net exporters of unfiltered methylmercury (Foe, 2003). Methylmercury 

concentrations were variable but high compared to concentrations in the river channels 

surrounding the islands from which the irrigation supply water was diverted and unused tailwater returned. Agricultural return flow concentrations averaged 0.35 ng/l in June and July 

2000 while concentration in the supply water was 0.07 ng/l; this translates to a net production 

rate of approximately 17 to 35 grams per month (~0.5 to 1.1 g/day) if occurring over the entire 

Delta or 10 to 25% of all river loading in the two-month period (Foe, 2003). 

The annual methylmercury load from agricultural lands located in the Delta was estimated to be 

123 g/yr (Table 6.2). Delta agricultural diversion and return flow estimates were obtained from 

the Delta Island Consumptive Use Model for water year 1999, the year during which the majority 

of agricultural drain methylmercury data were collected (Table 6.8); these flow estimates do not 

include the Yolo Bypass area north of the legal Delta. The annual diversion and return flow 

water volumes were multiplied by their respective methylmercury concentrations to estimate 

annual loads. For this preliminary evaluation, the average of available agricultural drain 

methylmercury data (Tables 6.6 and 6.7) was used to estimate methylmercury concentrations in 

all Delta agricultural return flows. The methylmercury concentration of river diversions was 

estimated by averaging monthly Sacramento River and State Water Project MeHg 

concentrations between May and December (Appendix D, Table D.3). To estimate the 

methylmercury loading from agricultural lands, the estimated methylmercury load in the river 

waters diverted onto the islands was subtracted from the agricultural return loads (Table 6.6), 

resulting in a net input of 123 grams per year. This load was multiplied by the percentage of 

total agricultural acreage located in each Delta subarea to estimate a subarea specific loading 

rate (Table 6.9). The Central Delta and Sacramento River subareas have the greatest 

estimated methylmercury loading from agricultural lands because they have the largest acreage 

of agricultural land. 

This evaluation indicates that agricultural runoff within the Delta and Yolo Bypass may 

contributes about 2.4% of the methylmercury load to the Delta/Yolo Bypass. 

A recent study evaluated methylmercury production on and discharges from eight farmed Delta 

islands (Farmed Islands). In exchange for access to the properties, the study authors did not 

include Farmed Island names or sampling locations in the report. The study results indicated 

that Farmed Islands in the northern/central Delta dominated by mineral soils had lower net 

methylmercury loads than Farmed Islands dominated by organic soils (Heim et al., October 

2009), with an overall annual loading rate (0.1 g/day x 365 = 36.5 g/yr) lower than that 

Delta Methylmercury TMDL Report 104 April 2010 
estimated by the above method for the WY2000-2003 period (123 g/yr). Even though there is a 

three-fold difference in the two methods’ resulting annual loads, their similarity is encouraging 

given very different method approaches and concentration data sets were used. In addition, 

both methods indicate that agricultural runoff contributes a relatively small portion of all 

methylmercury loading to the Delta/Yolo Bypass (2.4% versus about 1%). 

The Heim and others’ October 2009 study report evaluated runoff throughout the year, not just 

during the irrigation season. The study authors found that on an annual basis Farmed Islands 

throughout the Delta appear to be net sources of methylmercury to the Delta and that on a 

seasonal basis Farmed Islands appear to be net sources of MeHg during high flow periods 

(December to May) but net sinks during low flow periods (June to November). On two of the 

Farmed Islands that were studied, water was purposely siphoned onto the islands for winter 

flooding; these two islands showed a strong seasonal trend of elevated methylmercury 

concentrations during winter months, significantly higher than other islands studies. In contrast, 

a comparison of Tables 7 and 10 in Heim and others’ October 2009 study report indicates that 

several islands may act as net sink for methylmercury throughout the year, not just during the 

low flow months. During Phase 1 of the proposed implementation program outlined in 

Chapter 4 of the draft Basin Plan Amendment staff report, staff would need to work with the 

study authors and Farmed Island landowners to determine which specific areas in the Delta and 

Yolo Bypass are acting as a net source and which areas are acting as a net sink in order to 

update the TMDL methylmercury source analysis. 

Heim and others’ October 2009 study focused exclusively on farmed islands and did not 

evaluate upland areas in the periphery of the Delta. A review of the upland areas mapped in 

DWR’s Delta Atlas (DWR, 1995) indicates that upland areas may comprise about 20% or more 

of the Delta and Yolo Bypass. Staff recommends that a follow-up study be undertaken to 

characterize loads from the upland areas within and upstream of the legal Delta and, if elevated, 

determine the primary land uses responsible for methylmercury production. The study should 

be done in cooperation with agricultural interests in the Delta region. 

Delta Methylmercury TMDL Report 105 April 2010 
Figure 6.7: Agricultural Lands within the Statutory Delta Boundary and Yolo Bypass. 

Delta Methylmercury TMDL Report 106 April 2010 
Table 6.6: Values Used to Estimate MeHg 

Loads from Agricultural Lands 

within the Legal Delta Boundary 

 

Average 

MeHg Conc.

(ng/l) (a) 

Flow

(acre-feet/ 

yr) (b)

MeHg 

Load

(g/yr) 

Diversions: 0.071 1,597,880 139 

Ag Drain 

Returns: 0.352 603,546 262 

Net Ag Drain Input (g/yr): 123 

(a) Average agricultural drain methylmercury 

concentration obtained from Table 6.7. Average 

methylmercury concentration for diversion flows was 

estimated by averaging monthly Sacramento River 

and State Water Project MeHg concentrations 

during May through December (Appendix D). 

(b) Estimated annual average agricultural diversion and 

return flows were obtained from Table 6.8. 

Table 6.7: Delta Agricultural Main Drain 

Methylmercury Concentration Data (a)

Site 

Sample 

Date 

MeHg Conc. 

(ng/l)

Empire Tract Main Drain 6/26/00 0.093 

Empire Tract Main Drain 7/19/00 0.117 

Lower Jones Main Drain 6/26/00 0.302 

Staten Island Main drain 6/26/00 0.198 

Staten Island Main drain 7/19/00 0.094 

Twitchell Island Main Drain 6/26/00 0.387 

Twitchell Island Main Drain 7/19/00 1.500 

Twitchell Island Main Drain 6/30/03 0.292 (b)

Twitchell Island Main Drain 7/28/03 0.341 

Twitchell Island Main Drain 8/27/03 0.609 

Twitchell Island Main Drain 9/25/03 0.157 (b)

Upper Jones Main Drain 7/19/00 0.131 

(a) Source: Foe, 2003; Central Valley Water Board sampling, 

2003. 

(b) Average of laboratory replicates (0.289 and 0.294 ng/l on 

6/30/03 and 0.147 and 0.167 ng/l on 9/25/03). 

Table 6.8: Delta-wide Island Consumptive Use Estimates – 

Water Year 1999 (acre-feet) 

Period (a)

Diversions 

 + 

Seepage Return Flow 

Net Channel 

Depletion 

Oct-98 92,969 36,155 56,815 

Nov-98 74,202 34,988 39,213 

Dec-98 81,348 31,359 49,989 

Jan-99 (b) 42,180 111,661 -69,481 

Feb-99 (b) 34,044 120,960 -86,916 

Mar-99 57,306 43,410 13,896 

Apr-99 108,000 46,532 61,468 

May-99 193,317 67,944 125,373 

Jun-99 273,838 92,648 181,190 

Jul-99 353,800 120,147 233,653 

Aug-99 221,540 77,167 144,373 

Sep-99 141,560 53,197 88,364 

Annual 

Totals (b) 1,597,880 603,546 994,334 

(a) Diversion and return flow volumes were obtained from the Delta Island 

Consumptive Use Model (Suits, 2000). 

(b) Only months with positive depletion were used in the annual methylmercury 

load estimates because no methylmercury concentration data were 

available for the agricultural return drains during the coolest/wettest months. 

Delta Methylmercury TMDL Report 107 April 2010 
Table 6.9: Agricultural Acreage and Methylmercury Load Estimates by Delta Subarea 

Central 

Delta 

Cosumnes / 

Mokelumne 

River 

Marsh

Creek 

Sacramento 

River 

San 

Joaquin

River 

West

Delta 

Yolo 

BypassNorth (c)

Yolo 

BypassSouth TOTAL 

Acreage (a) 157,035 6,790 9,362 155,532 96,874 17,313 11,046 70,523 524,474

% of Total Acreage 30% 1.3% 1.8% 30% 18% 3.3% 2.1% 13% 100% 

Estimated Annual 

MeHg Load (g/year) (b) 36.8 1.6 2.2 36.4 22.7 4.1 2.6 16.5 123 

(a) Land cover source: DWR land use GIS coverages (1993-2003). 

(b) A Delta-wide agricultural land methylmercury loading of 123 g/yr was estimated using the information presented in Tables 6.6 

through 6.8. The Delta-wide load was multiplied by the percentage of total agricultural acreage located in each Delta subarea to 

estimate the amount of loading from agricultural lands in each subarea. 

(c) The Yolo Bypass-North subarea does not include agricultural areas in the Yolo Bypass north of the legal Delta boundary. 

6.2.5 Urban Runoff 

Approximately 60,000 acres of the land in the Delta and Yolo Bypass north of the legal Delta 

boundary is classified as urban (DWR, 1993-2003). Most of the urban area is regulated by 

waste discharge requirements under the National Pollutant Discharge Elimination System 

(NPDES), which permits discharge of storm water from municipal separate storm sewer 

systems (MS4s).35 Table 6.10 lists the permits that regulate urban runoff in the Delta and the 

amount of urban acreage in each Delta subarea. Figure 6.8 shows their locations. Urban 

acreages corresponding to each Permittee were estimated from the DWR Land Use coverage 

(DWR, 1993-2003) using available MS4 service area delineations. MS4 service area 

delineations for Sacramento, Stockton and Tracy are based on paper or electronic maps 

provided by the MS4 Permittees; all other MS4 service areas were delineated using 1990 city 

and county boundaries. Urban areas not encompassed by a MS4 service area were grouped 

into a “nonpoint source” category within each Delta subarea, consistent with USEPA’s 

requirements and guidance for establishing waste load allocations for storm water sources 

(USEPA, 2002). 

Methylmercury concentration data have been collected by Central Valley Water Board staff and 

the City and County of Sacramento from several urban waterways in or adjacent to the Delta. 

Figure 6.9 shows the sampling locations, Figure H.1 in Appendix H illustrates the wet and dry 

 

35 A municipal separate storm sewer system (MS4) is a conveyance or system of conveyances that include roads 

with drainage systems, municipal streets, alleys, catch basins, curbs, gutters, ditches, manmade channels, or 

storm drains, owned by a State, city, county, town or other public body. MS4s are designed and used for collecting 

or conveying storm water and do not include combined sewer systems or parts of a publicly owned treatment 

works. MS4s discharge to Waters of the United States. The Municipal Storm Water Permitting Program regulates 

storm water discharges from MS4s. MS4 permits were issued in two phases. Under Phase I, which started in 1990, 

the RWQCBs have adopted NPDES storm water permits for medium (serving between 100,000 and 250,000 

people) and large (serving greater than 250,000 people) municipalities. Most of these permits are issued to a 

group of co-permittees encompassing an entire metropolitan area. These permits are reissued as the permits 

expire. As part of Phase II, the State Board adopted a General Permit for the discharge of storm water from small 

MS4s (WQ Order No. 2003-0005-DWQ, NPDES No. CAS000004) to provide permit coverage for smaller 

municipalities, including non-traditional small MS4s, which are governmental facilities such as military bases, public 

campuses, and prison and hospital complexes. 

Delta Methylmercury TMDL Report 108 April 2010 
weather concentrations by location, and Appendix L provides the concentration data used in 

Figure H.1. Methylmercury concentrations ranged from a wet weather low of 0.035 ng/l (City of 

Sacramento Sump 111) to a dry weather high of 2.04 ng/l (Strong Ranch Slough). A visual 

inspection of the methylmercury data suggests that the differences between urban watersheds 

are not related to land use. Therefore, the data were averaged by wet and dry weather for each 

location (Table 6.11). The averages of these location-based wet and dry weather averages are 

assumed to represent runoff from all urban areas in or adjacent to the Delta and were used to 

estimate loads. These values are similar to methylmercury levels observed during high flow 

conditions in two urbanized tributaries in the Washington, D.C. region. The urbanized Northeast 

and Northwest Branches of the Anacostia River had average methylmercury concentrations of 

0.12 ± 0.06 ng/l and 0.07 ± 0.07 ng/l, respectively, during base flows, and 0.39 ± 0.21 ng/l and 

0.77 ± 0.46 ng/l, during high flows (Mason and Sullivan, 1998). 

Average annual urban runoff loading was estimated for WY2000-2003 so that urban runoff 

loading could be compared to tributary loading (Table 6.2). To estimate wet weather 

methylmercury loads, the wet weather concentration (0.241 ng/l) was multiplied by the runoff 

volumes estimated for WY2000-2003 for each MS4 area within each Delta subarea. To 

estimate dry weather methylmercury loads, the dry weather concentration (0.363 ng/l) was 

multiplied by the estimated dry weather urban runoff volume. Section E.2.3 in Appendix E 

describes the methods used to estimate wet and dry weather runoff volumes from urban areas 

within the Delta. Wet and dry weather methylmercury loads were summed to estimate the 

average annual loading of 20 grams to Delta waterways. The loading to each Delta subarea 

(Table 6.12) was used to develop MS4 Permittee and subarea-specific allocations (Chapter 8). 

Urban land use comprises a small portion of the surface area in the Delta and contributes only 

about 0.4% of the Delta methylmercury load (Table 6.2). In contrast, approximately 

320,000 acres of urban land – about 42% of all urban area within the Delta source region – 

occur within 20 miles of the statutory Delta boundary, about one day water travel time upstream. 

In addition, some of the urban watersheds outside the Delta discharge via sumps into Delta 

waterways. These discharges were not included in the Delta load estimate. As a result, the 

urban contribution to the Delta methylmercury load may be underestimated. 

To evaluate the potential contributions from upstream urban lands, the methylmercury loadings 

from the two MS4 service areas with the greatest urban acreage immediately upstream of the 

Delta were estimated. The sum of methylmercury loads from the Sacramento and Stockton 

MS4 areas may contribute about 1% of methylmercury loading to the Delta (Table 6.13). These 

loads are expected to increase as urbanization continues around the Delta. 

Delta Methylmercury TMDL Report 109 April 2010 
Table 6.10: Urban Acreage and MS4 Permits that Regulate Urban Runoff within the Delta/Yolo Bypass. 

Urban Acreage within Delta Subareas (b)

Permittee NPDES # (a) Central 

Delta 

Marsh

Creek 

Mokelumne 

/ Cosumnes 

Rivers 

Sacramento

River 

San 

Joaquin 

River 

West 

Delta 

Yolo 

Bypass (c)

Total 

Acreage

Contra Costa County CAS083313 2,181 3,427 9,518 15,126 

Lathrop (City of) CAS000004 738 738 

Lodi (City of) CAS000004 134 134 

Port of Stockton CAS084077 1,067 28 1,095 

Rio Vista (City of) CAS000004 37 37 

Sacramento Area MS4 (d) CAS082597 4,766 4,766 

San Joaquin County CAS000004 1,494 121 521 6,040 8,176 

Solano County CAS000004 181 220 401 

Stockton MS4 Permit Area CAS083470 10,574 1,481 12,055 

Tracy (City of) CAS000004 5,268 5,268 

West Sacramento (City of) CAS000004 1,824 2,756 4,580 

Yolo County CAS000004 200 796 966 

Urban Nonpoint Source (e) 337 44 1,615 7 231 2,234 

Total Acreage 15,787 3,427 165 9,144 13,562 9,749 3,772 55,606 

(a) Permittees with NPDES No. CAS000004 are covered under the General Permit for the discharge of storm water from small MS4s 

(WQ Order No. 2003-0005-DWQ) adopted by the State Water Board to provide permit coverage for smaller municipalities 

(serving less than 100,000 people). 

(b) Urban land uses and acreages corresponding to each Permittee were estimated from the DWR Land Use coverage (DWR, 1993-

2003) using available service area delineations. MS4 service area delineations for Sacramento, Stockton and Tracy are based 

on paper or electronic maps provided by the MS4 Permittees; all other MS4 service areas were delineated using 1990 city 

boundaries. 

(c) The Yolo Bypass subarea includes urban areas in the Yolo Bypass north of the legal Delta boundary. 

(d) The Sacramento MS4 Area does not include the Sacramento Combined Sewer System (CSS) service area illustrated in 

Figure 6.8. The CSS service area is permitted by a separate NPDES permit, which is described in Section 6.2.3 and Table G.2 in

Appendix G. 

(e) Urban areas not encompassed by a MS4 service area were grouped into the “nonpoint source” category. 

Delta Methylmercury TMDL Report 110 April 2010 
Figure 6.8: NPDES Permitted Municipal Separate Storm Sewer System (MS4) Areas in the Delta Region. 

(Only those MS4 areas that intersect the statutory Delta boundary and Yolo Bypass are labeled. 

MS4 service area delineations for Sacramento, Stockton and Tracy are based on paper or electronic 

maps provided by the MS4 Permittees; all other MS4 service areas were delineated using 

1990 city or county boundaries.) 

Delta Methylmercury TMDL Report 111 April 2010 
Figure 6.9: Urban Areas and Aqueous MeHg Sampling Locations in the Delta Region. 

Delta Methylmercury TMDL Report 112 April 2010 
Table 6.11: Summary of Urban Runoff Methylmercury Concentrations

Location 

# of 

Samples 

Minimum 

Conc. (ng/l)

Average 

Conc. (ng/l)

Maximum 

Conc. (ng/l)

DRY WEATHER

Arcade Creek 9 0.099 0.358 1.213 

Sacramento Strong Ranch Slough 2 0.158 1.099 2.040 

Sacramento Sump 104 2 0.088 0.093 0.097 

Sacramento Sump 111 2 0.135 0.176 0.217 

Tracy Lateral to Sugar Cut Slough 1 0.091 0.091 0.091 

Average of Location Averages: 0.363 ng/l 

WET WEATHER

Arcade Creek 7 0.099 0.240 0.339 

Sacramento Strong Ranch Slough 4 0.237 0.522 0.878 

Sump 104 4 0.153 0.290 0.610 

Sump 111 4 0.035 0.212 0.420 

Stockton Calaveras River Pump Station 5 0.105 0.167 0.301 

Stockton Duck Creek Pump Station 1 0.103 0.103 0.103 

Stockton Mosher Slough Pump Station 4 0.084 0.125 0.189 

Stockton Smith Canal Pump Station 4 0.099 0.263 0.533 

Tracy Drainage Basin 10 Outflow 3 0.103 0.192 0.257 

Tracy Drainage Basin 5 Outflow 3 0.110 0.138 0.191 

Tracy Lateral to Sugar Cut Slough 3 0.040 0.400 0.918 

Average of Location Averages: 0.241 ng/l 

Table 6.12: Average Annual Methylmercury Loading from Urban Areas within Each Delta Subarea 

for WY2000-2003 

DELTA SUBAREA (g/yr)

MS4 PERMITEE Central 

Delta 

Marsh

Creek 

Mokelumne 

/ Cosumnes 

Rivers 

Sacramento 

River 

San Joaquin 

River 

West 

Delta 

Yolo 

Bypass 

Grand

Total 

(g/yr)

Contra Costa County 0.75 1.2 3.2 5.2 

Lathrop (City of) 0.27 0.27 

Lodi (City of) 0.053 0.053 

Port of Stockton 0.39 0.010 0.40 

Rio Vista (City of) 0.014 0.014 

Sacramento Area MS4 1.8 1.8 

San Joaquin County 0.57 0.045 0.19 2.2 3.0 

Solano County 0.073 0.085 0.16 

Stockton MS4 Permit Area 3.6 0.50 4.1 

Tracy (City of) 1.8 1.8 

West Sacramento (City of) 0.65 1.1 1.8 

Yolo County 0.073 0.33 0.40 

Urban Nonpoint Source 0.14 0.018 0.63 0.0022 0.066 0.85 

Grand Total 5.5 1.2 0.063 3.4 4.8 3.3 1.5 20 

Delta Methylmercury TMDL Report 113 April 2010 
Table 6.13: Comparison of Sacramento and Stockton Area MS4 

Methylmercury Loading to Delta Methylmercury 

Loading for WY2000-2003. 

MS4 Service Area (a)

Water Volume

(M acre-feet) (b) MeHg Load (grams/year) 

Sacramento MS4 Urban Total 0.18 59 

Stockton MS4 Urban Total 0.026 8.6 

Total Delta Inputs (c) 20 5,219 

Stockton & Sacramento Runoff 

as % of Total Delta Inputs 1.0% 1.3% 

(a) The Sacramento and Stockton Area MS4s are the two MS4 service areas 

with the greatest urban acreage in the greater Delta region, with urban land 

use areas of about 161,000 and 25,000 acres, respectively. 

(b) Refer to Section E.2.3 in Appendix E for urban runoff volume estimates for 

wet and dry weather, which were summed to estimate the annual average 

water volumes shown above. 

(c) These values represent the sum of all tributary inputs and within-Delta 

methylmercury sources shown in Table 6.2. 

6.2.6 Atmospheric Deposition 

At the time the TMDL was developed, atmospheric deposition of methylmercury had not yet 

been measured within the Delta. However, several published papers provided reviews of 

methylmercury levels in wet deposition in a variety of locations around the world 

(e.g., Nguyen et al., 2005; Lawson and Mason, 2001; Mason et al., 1997 and 2000). These 

reviews indicate that the ratios of methyl to total mercury concentrations in wet deposition range 

from 0.25 to 6%, and that typically less than 1% of total mercury in wet deposition is 

methylmercury. As described in Section 7.1.4 and Table 7.1, total mercury loading from wet 

deposition to Delta water surfaces and land surfaces not including urban areas was estimated 

to be 2,318 g/yr for WY2000-2003. A methyl to total mercury ratio of 1% was used to estimate 

the mass of methylmercury deposited by wet deposition: 

Equation 6.2: 

 MeHg Mass = Total mercury mass * MeHg:TotHg 

23 g/yr = 2.3 kg/year * 0.01 

Table 6.14 provides the methylmercury load estimates for atmospheric deposition to each Delta 

subarea. Wet deposition in the Delta and Yolo Bypass likely contributes less than 1% of all 

methylmercury entering the Delta (Table 6.2). Therefore, it is assumed that atmospheric input 

to waterways and land surfaces within the Delta and Yolo Bypass is not a significant source of 

methylmercury. A recently completed CalFed study similarly found that atmospheric inputs 

within the Delta contribute less than 1% of all methylmercury entering the Delta (Foe et al., 

2008). Methylmercury in wet deposition to urban land surfaces was not evaluated because it is 

incorporated in the estimates for loading from urbanized lands described in Section 6.2.5. 

Delta Methylmercury TMDL Report 114 April 2010 
Table 6.14: Estimate of Average Annual Methylmercury Loading from Wet Deposition 

Delta Subarea 

WY2000-2003 Average 

Annual TotHg Load (g/yr) (a) Estimated MeHg Load 

(g/yr) (b)

Central Delta 729 7.3 

Marsh Creek 23 0.23 

Mokelumne / Cosumnes River 29 0.29 

Sacramento River 560 5.6 

San Joaquin River 272 2.7 

West Delta 237 2.4 

Yolo Bypass-North (c) 100 1.0 

Yolo Bypass-South 315 3.2 

TOTAL 2,265 (2.3 kg/yr) 23 

(a) Total mercury loading from precipitation on surface water and non-urbanized land surfaces in the Delta 

and Yolo Bypass was estimated by multiplying the average mercury concentration in North Bay/Martinez 

rainwater by the average rainfall runoff volume during WY2000-2003 (see Section 7.1.4 in Chapter 7 

and Section E.2.3 in Appendix E). 

(b) The published literature indicates that ratios of methyl to total mercury concentrations in wet deposition 

typically range from 0.25% to 6%, and that typically less than 1% of total mercury in wet deposition is 

methylmercury. A methyl to total mercury ratio of 1% was used to estimate the mass of methylmercury 

deposited to waterways in each subarea. 

(c) The Yolo Bypass-North subarea includes areas in the Yolo Bypass north of the legal Delta boundary. 

6.2.7 Other Potential Sources 

Potential methylmercury sources in the Delta/Yolo Bypass not evaluated by this TMDL may 

include the following: 

• Methylmercury flux from floodplain sediments when floodplains are inundated; 

• Agricultural areas in the Yolo Bypass north of the legal Delta boundary; 

• Rainwater runoff from agricultural areas throughout the Delta and Yolo Bypass; and 

• Runoff from rangeland and other open-space areas not encompassed by urban, wetland, 

or agricultural areas. 

• Return water from dredge material disposal ponds. 

The methylmercury load estimates for methylmercury flux from open water sediments described 

in Section 6.2.2 do not address floodplain acreage that is not permanently inundated. As 

illustrated in the Sacramento-San Joaquin Delta Atlas (DWR, 1995), the Delta encompasses a 

maze of over 1,100 miles of river channels that are almost entirely constrained by local and 

federal flood control project levees. Throughout the Delta, there is very little acreage between 

channel levees not already included in the wetland and open water acreages, with the exception 

of the Yolo Bypass. The Yolo Bypass is a massive floodplain (about 73,000 acres) on the west 

side of the lower Sacramento River that receives floodwaters routed from the Sacramento and 

Feather Rivers by the Fremont and Sacramento Weirs (see Section E.2.2 and Figure E.2 in 

Appendix E). The Yolo Bypass typically floods in more than half of water years, for an average 

Delta Methylmercury TMDL Report 115 April 2010 
of two months every other year; complete inundation of the floodplain approximately doubles the 

wetted area of the Delta and is equivalent to about one-third the area of San Francisco and San 

Pablo bays (Sommer et al., 2001; Foe et al., 2008). The WY2000-2003 period that 

encompasses the available methylmercury concentration data for the major Delta inputs and 

exports was a relatively dry period. However, bypass floodplain inundation may contribute 

substantial methylmercury loading to the Delta. Results from a recent CalFed study indicate 

that inundated areas in the Yolo Bypass are potentially large sources of methylmercury to the 

bypass and Delta (Foe et al., 2008). Board staff will include results from this and other 

floodplain habitat studies completed during the first phase of TMDL implementation when the 

source analysis is re-evaluated during the Delta mercury control program review. 

As noted in Section 6.2.4, the agricultural return flows upon which the return flow methylmercury 

load estimates are based do not include the Yolo Bypass area north of the legal Delta or other 

upland areas in the Delta periphery. In addition, the load estimates address only runoff during 

the active irrigation season because no methylmercury concentration data were available for 

stormwater runoff from agricultural areas at the time the TMDL was developed. Staff 

recommends that the following activities take place during the first phase of the proposed 

implementation program outlined in Chapter 4 of the draft Basin Plan Amendment staff report in 

order to improve the source analysis: 

• Work with the study authors of the recent Farmed Islands study (Heim et al., 2009) and 

Farmed Island landowners to determine which specific areas in the Delta and Yolo 

Bypass are acting as a net source and which areas are acting as a net sink on an annual 

basis. 

• Undertake a follow-up study to characterize loads from farmed land in upland areas in the 

Delta region and, if elevated, determine the primary land uses responsible for 

methylmercury production, in cooperation with agricultural interests in the Delta region. 

Similarly, methylmercury concentration data were not available for stormwater runoff from 

rangeland and other upland areas not encompassed by urban, wetland, water, or agricultural 

load estimates. Because such upland areas comprise only about 8% of land cover within the 

Delta and Yolo Bypass, they are not expected to contribute substantially more methylmercury 

loading than that already present in rainfall, which was estimated for this TMDL. However, such 

upland areas could account for more of the methylmercury loading to tributary watersheds. 

Staff recommends that upstream TMDL program studies incorporate analyses of methylmercury 

in runoff from upland areas. 

As discussed in the following section, sediment is dredged at various locations in the Delta to 

maintain ship channels and marinas. Dredge material typically is pumped to either disposal 

ponds on Delta islands or upland areas. At the time that the TMDL was developed, no 

methylmercury data were available for return flows to the Delta/Yolo Bypass from dredge 

material disposal (DMD) ponds. Since the February 2008 draft report was released, 

methylmercury monitoring took place at five DMD ponds in the Delta to determine whether DMD 

ponds produce methylmercury that could be discharged to Delta waterways (AMS, 2010). 

Samples of pond water, representing water that would leave the DMD ponds if discharge 

occurred, were collected approximately every 10 days for 40 days after dredge disposal. 

Monitoring indicated the following: 

Delta Methylmercury TMDL Report 116 April 2010 
• Average and median methylmercury concentrations in samples representing DMD pond 

outflows were about 10x to >100x higher than what is observed in receiving waters. 

Sacramento River and San Joaquin Rivers average 0.11 and 0.18 ng/l, respectively, per 

a recent CalFed study (Foe et al., 2008). Average DMD pond outflow methylmercury 

concentrations were 1.1, 1.5, 5.9, 9.6 and 20.8 ng/l for the five ponds. 

• The methylmercury concentration in all sampled DMP site ponds increased above inflow 

levels during the monitoring effort, which likely indicates that methylmercury was 

produced at the sites. 

During the first phase of TMDL implementation, Board staff will need to work with U.S. Army 

Corps of Engineer staff and contractors to determine how to estimate the volume of DMD pond 

return flows to the Delta/Yolo Bypass during a range of dredging project years (e.g., during 

some years there may be little-to-no discharge from the DMD ponds) in order to estimate the 

amount of methylmercury produced by the DMD ponds and methylmercury loads discharged to 

the Delta/Yolo Bypass. New information will be incorporated in the TMDL when the source 

analysis is re-evaluated during the Delta mercury control program review. 

6.3 Methylmercury Losses 

The following were identified as contributing to methylmercury losses from the Delta: water 

exports to southern California, outflow to San Francisco Bay, removal of dredged sediments, 

photodegradation, biotic uptake and other loss terms. Table 6.15 lists the average 

methylmercury concentrations and estimated average annual loads associated with the losses 

for the WY2000-2003 period, a relatively dry period that encompasses the available 

concentration data for the major Delta inputs and exports. Figure 6.10 shows the aqueous 

monitoring locations for major methylmercury exports and the approximate locations of recent 

dredging projects. 

Figures and tables cited in Sections 6.3.1 through 6.3.4 are arranged after Section 6.3.4 in the 

order in which they were mentioned. 

Table 6.15: Methylmercury Concentrations and Loads Lost from the Delta 

for WY2000-2003.

Average 

Annual 

Load 

(g/yr) % All MeHg

Average 

Aqueous 

Concentration

(ng/l) 

Outflow to San Francisco Bay (X2) 1,717 69.7% 0.08 

Dredging 341 13.9% - - - 

State Water Project 203 8.2% 0.05 

Delta Mendota Canal 201 8.2% 0.06 

Photodegradation To Be Determined 

Accumulation in Biota Unknown 

TOTAL EXPORTS: 2,462 g/yr (2.5 kg/yr) 

Delta Methylmercury TMDL Report 117 April 2010 
6.3.1 Outflow to San Francisco Bay 

Outflow to San Francisco Bay is the primary way that methylmercury is lost from the Delta. 

Methylmercury in Delta outflow to San Francisco was evaluated by collecting samples at X2. 

X2 is the location in the Bay-Delta Estuary with 2 parts per thousand (o/oo) bottom salinity. The 

location of X2 moves as a function of both tidal cycle and freshwater inflow, typically between 

the Cities of Martinez and Pittsburg, west of the legal Delta boundary. This salinity was chosen 

because 2 to 3 o/oo salinity is the normal osmotic tolerance of freshwater organisms, and a goal 

of the CALFED studies was to estimate the methylmercury exposure of these organisms. 

Staff from the Central Valley and San Francisco Bay Central Valley Water Boards has agreed to 

consider Mallard Island as the boundary between the two regions for control of mercury. The 

site was selected as it is near the legal boundary and has a U.S. Geological Survey flow gauge. 

Central Valley Water Board staff conducted monthly aqueous methylmercury sampling at X2 

from March 2000 to September 2001 (Foe, 2003) and from April to September 2003. 

Figure 6.11 and Table 6.16 summarize the export data. Methylmercury concentrations at X2 

averaged 0.075 ng/l and ranged from below detection limits to 0.241 ng/l. Net daily Delta 

outflow water volumes were obtained from the Dayflow model (Section E.2.4 in Appendix E). 

Methylmercury concentrations for X2 and net daily Delta outflows were regressed against each 

other to determine whether flow could be used to predict methylmercury concentration 

(Appendix F). The regression was significant at P<0.05 and accounted for about 20% of the 

variation in methylmercury concentrations. The regression-based export load was 2,086 g/yr. 

An alternate approach is to use average monthly methylmercury concentrations to estimate 

Delta exports. Concentration data were pooled by month to calculate monthly average 

concentrations for WY2000-2003 (Table F.1 in Appendix F). Monthly average concentrations 

were multiplied by monthly average flows for WY2000-2003 to estimate monthly loads and 

summed to calculate an annual average methylmercury load for WY2000-2003 of 1,717 g/yr. 

The latter estimate appears similar to the regression-based estimate (2,086 g/yr). Table 6.15 

uses an advective export rate of 1,717 g/yr to San Francisco Bay. This accounts for 

approximately 70% of identified Delta methylmercury losses from exports to San Francisco Bay 

and south of the Delta (via State Water Project and Delta Mendota Canal) and sediment 

removal by dredging activities. No attempt was made to estimate dispersive loads. It is not 

known whether dispersive or tidal flows would increase or decrease the net methylmercury load 

exported to the Bay area. The results from a recently completed CalFed study (Foe et al., 

2008) indicate that the methylmercury load exported to San Francisco Bay may be much 

greater (3,577 g/yr; see Figure 9 in Foe et al., 2008), when data for wet years are incorporated 

in the load calculations. 

6.3.2 South of Delta Exports 

Water diversions to southern California account for approximately 16% of identified Delta 

methylmercury losses from exports to San Francisco Bay and south of the Delta (via State 

Water Project and Delta Mendota Canal) and sediment removal by dredging activities 

(Table 6.15). Methylmercury in Delta Mendota Canal (DMC) and State Water Project (SWP) 

exports to southern California were evaluated by collecting water samples from the DMC canal 

Delta Methylmercury TMDL Report 118 April 2010 
off Byron Highway (County Road J4) and from the input canal to Bethany Reservoir, 

respectively. Bethany is the first lift station on the State Water Project canal system and is 

about one mile south of Clifton Court Forebay in the Delta. Figure 6.10 illustrates the sampling 

locations. 

Central Valley Water Board staff conducted monthly methylmercury sampling at the DMC and 

SWP from March 2000 to September 2001 (Foe, 2003) and from April 2003 to April 2004. 

Appendix L provides the methylmercury concentration data collected at the DMC and SWP and 

Figure 6.11 and Table 6.16 summarize methylmercury concentrations. The volume of water 

exported by the DMC and SWP was obtained from the Dayflow model (Section E.2.4 in 

Appendix E). Like at X2, methylmercury concentrations were regressed against daily flow to 

determine whether the concentrations could be predicted from the flow (Appendix F). Neither 

regression was significant (P<0.05). Therefore, average methylmercury concentrations of 0.05 

and 0.06 ng/l (Table 6.16) were used to estimate SWP and DMC export loads of 203 and 

201 g/yr, respectively (Table 6.15). A recently completed CalFed study (Foe et al., 2008) found 

average methylmercury concentrations of 0.07 and 0.10 ng/l for the SWP and DMC, 

respectively, and slightly higher annual methylmercury loads (548 g/yr for the sum of SWP and 

DMC exports; see Figure 9 in Foe et al., 2008), when data for wet years were incorporated. 

6.3.3 Export via Dredging 

Sediment is dredged at various locations in the Delta to maintain ship channels and marinas. 

No data have been gathered on methylmercury levels in dredge material removed from the 

Delta. To determine whether dredging activities could result in notable methylmercury loss from 

the Delta, a preliminary load estimate was developed using available dredge volume and total 

mercury information and surficial sediment methylmercury concentration data. Methylmercury 

removed by dredge activities could account for almost 14% of the identified methylmercury 

losses from exports to San Francisco Bay and south of the Delta (via State Water Project and 

Delta Mendota Canal) and sediment removal by dredging activities (Table 6.15). 

Dredge material is typically pumped to either disposal ponds on Delta islands or upland areas. 

Table 6.17 provides information for recent dredge projects within the Delta and Figure 6.10 

shows their approximate locations. The Sacramento and Stockton deep water channels have 

annual dredging programs; the locations dredged each year vary. Dredging occurs at other 

Delta locations when needed, when funds are available, or when special projects take place. 

Approximately 533,400 cubic yards of sediment are dredged annually on average, with 199,000 

cubic yards from the Sacramento Deep Water Ship Channel and 270,000 cubic yards from the 

Stockton Deep Water Channel. Other minor dredging projects at marinas remove sediment at 

various frequencies for a combined total of about 64,400 cubic yards per year. Average 

mercury concentrations in the sediment for the project sites range from 0.04 to 0.41 mg/kg (dry 

weight). The annual mass of mercury removed from the Delta through dredging projects is 

approximately 57 kg/year. Section 7.2.3 provides a description of the methods used to estimate 

the annual mass of total mercury removed by dredging and the uncertainty in the estimate. 

None of the dredging projects analyzed sediment samples for methylmercury. Heim and others 

(2003) evaluated surficial sediment MeHg:TotHg at several locations in the Sacramento and 

Stockton Deep Water Channels (Table 6.18), where nearly 90% of all dredged materials from 

Delta Methylmercury TMDL Report 119 April 2010 
the Delta are removed. The average MeHg:TotHg of 0.006 was used to estimate the mass of 

methylmercury removed by dredging projects: 

Equation 6.3: 

 MeHg Mass = Total mercury mass * MeHg:TotHg 

 341 g/yr = 57 kg/year * 1000 (g/kg) * 0.006 

Use of surficial sediment MeHg:TotHg to estimate methylmercury mass removed by dredging 

assumes that MeHg:TotHg is consistent throughout all depths of sediment in the dredged areas, 

which may overestimate the mass removed if methylmercury levels actually decrease with 

depth. In addition, methylmercury production may increase after dredging activities if the newly 

exposed sediment has higher total mercury concentrations. Central Valley Water Board staff 

recommends that dredgers quantify the amount of methylmercury removed, determine the 

mercury concentration of fine grain material in newly exposed sediment, and monitor 

methylmercury production at dredge material disposal and reuse areas (see previous discussion 

in Section 6.2.7 in this chapter and Chapter 4 in the draft Basin Plan Amendment staff report). 

6.3.4 Other Potential Loss Pathways 

Possible methylmercury loss processes within the Delta include degradation by sunlight 

(photodegradation), particle settling, and accumulation by biota. Data collected after the TMDL 

source analysis was completed show that photodegradation and particle settling are important 

processes that can account for the within-Delta losses (Stephenson and Bonnema, 2008; Gill, 

2008a). Photodegradation rates vary with depth of light penetration into water and hours of 

sunlight. On average at four locations in the Delta, loss by photodegradation was 

2.5 g methylmercury/day, or 13% of the average daily input of methylmercury (Gill, 2008a). In 

the Sacramento River near Rio Vista, the photodegradation rate was about 4 g/day or 30% of 

the dissolved methylmercury per day at the top half meter of water (Byington et al., 2005). 

Results in the Delta are similar to photodegradation rates observed in Florida and Canada. 

Methylmercury photodegradation rates in a boreal forest lake in northwestern Ontario, Canada, 

ranged between -3 and 27% per day, with the highest rates at the lake surface (Sellers and 

Kelly, 2001). In the Everglades, Krabbenhoft and others (1999) observed methylmercury 

degradation rates ranging from 2 to 15% per day. Krabbenhoft and others (1999 and 2002) also 

found that the majority of photodegradation occurred in the top half meter of water; however, 

they also found that the rate of degradation was largely dependent on the concentration of 

dissolved organic carbon. The large surface to depth ratio of the Delta, coupled with its 

relatively long residence time, may result in significant loss of methylmercury by 

photodegradation. 

Settling of particles in the Delta creates significant methylmercury loss because the Delta is a 

sink for incoming sediment and more than half of the methylmercury is bound to particulates 

(Foe et al., 2008). In CalFed studies completed after the TMDL source analysis, particle settling 

removed methylmercury at an average rate of 25% of incoming loads (Stephenson and 

Bonnema, 2008). Methylmercury loss due to sedimentation is flow-dependent, meaning more 

methylmercury is lost during winter (usually higher flows) than in summer. 

Delta Methylmercury TMDL Report 120 April 2010 
The amount of methylmercury accumulating in aquatic biota is not known. However, studies 

could be undertaken to ascertain the rate of transfer from the abiotic to the biotic component of 

the food web. 

Table 6.16: Methylmercury Concentrations for the Delta’s Major Exports 

Site 

# of 

Samples 

Min. MeHg 

Conc. (ng/l) (a)

Ave. MeHg 

Conc. (ng/l)

Annual Ave. 

Conc. (ng/l) (b)

Median MeHg 

Conc. (ng/l)

Max. MeHg 

Conc. (ng/l)

Delta Mendota Canal 21 ND 0.062 0.064 0.061 0.171 

State Water Project 20 ND 0.051 0.054 0.049 0.144 

Outflow to San 

Francisco Bay (X2) 22 ND 0.075 0.083 0.070 0.241

(a) ND: below method detection limit. 

(b) Sampling of these exports took place between March 2000 and September 2003. Methylmercury concentration data were 

pooled by month to estimate monthly average methylmercury concentrations and loads (Table F.1 in Appendix F); the monthly 

average loads were summed to estimate annual average methylmercury loads for water years 2000-2003. The monthly 

average concentrations were averaged to estimate annual average concentrations, which were included in Table 6.15. 

Space intentionally left blank.

Delta Methylmercury TMDL Report 121 April 2010 
Figure 6.10: Aqueous Monitoring Locations for Major Methylmercury Exports and 

Approximate Locations of Recent Dredging Projects. 

Delta Methylmercury TMDL Report 122 April 2010 
Delta Mendota Canal

0

0.1

0.2

0.3

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MMHg Conc. (ng/l)

State Water Project

0

0.1

0.2

0.3

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MMHg Conc. (ng/l)

Delta Outflow s to San Francisco Bay

0

0.1

0.2

0.3

Mar-00 Mar-01 Mar-02 Mar-03 Mar-04

MMHg Conc. (ng/l)

Figure 6.11: Available Methylmercury Concentration Data for the Delta’s Major Exports 

Delta Methylmercury TMDL Report 123 April 2010 
Table 6.17: Recent Dredge Projects within the Delta. 

Delta Dredging 

Project 

Project 

Location 

Volume 

of 

Dredge 

Material 

(cubic 

yards) 

Dredge 

Frequency 

Disposal 

Location 

(upland, Delta 

island, wetland 

areas, etc.) 

Mean 

Sediment 

Mercury 

Conc. (mg/kg, 

dry wt) (a)

# of 

Samples

Standard 

Dev. 

T Value 

(p=0.975, 

conf 95%, 

df =n-1) 

Total 

Weight of 

Mercury 

Removed 

(kg) 

Annual Weight 

of Mercury 

Removed (a) 

(kg) 

Annual 

Weight of Sediment 

Removed 

(Mkg, 

dry wt) 

Sac. River 

Deep Water 

Ship Channel (b)

Sacramento 

River 199,000 Annually Delta Island/ upland 0.37 ±3.93 2 0.4377 12.71 42 42 ±446 (n) 110.5 

Stockton 

Deep Water 

Channel (c)

San Joaquin 

River 270,000 Annually Delta Islands 0.083 ±0.023 28 0.0594 2.052 13 13 ±3.5 150.0 

Village West 

Marina (d)

14-Mile 

Slough 70,000 Every 10 years Delta Islands 0.043 ±0.014 3 0.0058 4.303 1.7 0.2 ±0.057 3.9 

KFM (e) San Joaquin River 3,000 One time Upland Unknown 1.7 

Korths Pirates 

Lair (f)

Mokelumne 

River 15,000 Every 5 years Upland 0.15 ±0.11 2 0.0120 12.71 1.3 0.25 ±0.18 1.7 

Big Break 

Marina (g) San Joaquin River 12,000 Every 5 years Upland 0.41 ±0.24 6 0.2318 2.571 2.8 0.55 ±0.33 1.3 

Sportsman 

Yacht 

Club (h)

San Joaquin 

River 10,000 Every 5 years Upland 0.12 ±0.014 3 0.0058 4.303 0.70 0.14 ±0.016 1.1 

Discovery Bay (i) Delta 50,000 (j) Annually Upland 0.027 ±0.018 7 0.0195 2.447 0.78 0.78 ±0.51 27.8 

Annual Averages (m) 533,400 cubic yards 57 ±451 kg (n) 349 Mkg 

(a) The uncertainty of the mercury load values was estimated by calculating the 95% confidence interval for the mean of the concentration data for each proje(b) U.S. Army Corps of Engineers, 2002 NOI (Notice of Intent) Sacramento DWSC. (c) U.S. Army Corps of Engineers, 2000-2003 NOI Stockton DWSC. (d) DCC Engineering Co, Inc., Village West Dredge Material Test, September 5, 2000. (e) KFM, 401 Water Quality Certification. (f) Anderson Engineers, 2003 Sediment Sampling and Analysis Plan for Korths Pirates Lair. (g) Subsurface Consultants, Inc., Environmental Site Assessment 2001 & Aquifer Sciences, Inc., Pre-Dredge Sampling and Analysis Plan July 29, 2003. (h) Padre Associates, Inc., Laboratory Analytical Results of Proposed Dredge Material and Associated Waste Classification May 23, 2003. (i) Kennetic Laboratories/ToxScan, Inc., Sediment Properties and Chemistry April 2002, Discovery Bay, 2003 Final Water Quality Monitoring Report, WDR O(j) Discovery Bay assumptions: The initial dredge project was 153,000 cubic yards, and 50,000 cubic yards/year thereafter. Therefore, assume 50,000 cy/yea

(k) WDR Order N. R5-2003-0027 indicates effluent returned to Discovery Bay averaged 3 mgd for several days to several weeks; staff assumed discharge pe

(l) Two dredging projects, Village West Marina and Discovery Bay, had effluent that returned to Delta waters. The volume of effluent returned to receiving wa

was approximately 42 million gal/year. The volume of effluent returned by the Village West Marina project is unknown. Staff estimated that the annual weDiscovery Bay dredge effluent was 0.008 kg, assuming that all water was returned. 

(m) Annual averages do not include KFM, a one-time project. 

(n) The uncertainty associated with the amount of mercury removed by dredging in the Sacramento Deep Water Ship Channel is particularly substantial (±446 

calculation being based on only two sample results (0.68 and 0.061 mg/kg mercury) that have a tenfold range. 

Delta Methylmercury TMDL Report 124 
Table 6.18: MeHg:TotHg in Deep Water Ship Channel Surficial Sediments 

 MeHg Conc. (ng/g) TotHg Conc. (ng/g) MeHg:TotHg Ratio 

Sacramento Deep Water Ship Channel (a)

Sacramento River DWSC 0.49 194.70 0.0025 

Stockton Deep Water Channel (a)

Little Connection Slough 0.20 82.51 0.0024 

Headreach Cutoff 1.86 89.46 0.0208 

Port of Stockton Turnabout #1 0.32 193.78 0.0017 

Port of Stockton Turnabout #2 0.32 130.30 0.0025 

AVERAGE RATIO: 0.006 

(a) Source: Heim et al., 2003. Latitude/longitude coordinates provided with the above samples indicated that these were 

collected within the dredged deep water ship channels. 

6.4 Delta Methylmercury Mass Budget & East-West Concentration Gradient 

Figure 6.12 illustrates the Delta’s average daily methylmercury imports and exports based on 

the annual loads presented in Tables 6.2 and 6.15. In situ sediment production and tributary 

water bodies account for about 35 and 58%, respectively, of methylmercury inputs to the Delta 

during the relatively dry WY2000-2003 period. Agricultural return flow and NPDES-permitted 

wastewater treatment plants contribute about 6% of the load while runoff from urban areas 

within the Delta/Yolo Bypass contributes about 0.4%. 

The difference between the sum of known inputs and exports is a measure of the uncertainty of 

the loading estimates and of the importance of other unknown processes at work in the Delta. 

As noted in Section 6.2, the sum of WY2000-2003 water imports and exports balances within 

approximately 5%, indicating that all the major water inputs and exports have been identified. In 

contrast, the methylmercury budget does not balance. Average annual methylmercury inputs 

and exports were approximately 14.3 g/day (5.2 kg/yr) and 6.7 g/day (2.5 kg/yr), respectively 

(Tables 6.2 and 6.15 and Figure 6.12). Exports are only about 50% of inputs, suggesting that 

the Delta acts as a net sink for methylmercury. 

A special study was conducted in the summer of 2001 to ascertain the location where much of 

the decrease in methylmercury occurred (Foe, 2003). Three transects were run down the 

Sacramento River and out toward San Francisco Bay, the water path from the main tributary 

source (Sacramento River) to the main export of methylmercury (Suisun Bay). The largest 

decrease in concentration consistently occurred in the vicinity or immediately downstream of Rio 

Vista (Figure 6.13). The drop in concentration was between 30 and 60%. Later studies funded 

by CalFed showed that losses from photodegradation and settling of methylmercury bound to 

particulates are of sufficient magnitude to explain the methylmercury decrease across the Delta 

(Gill, 2008a; Stephenson and Bonnema, 2008). For example, as described in the previous 

section, preliminary photodegradation study results for the Sacramento River near Rio Vista 

indicate relative surface water photodegradation rates of about 30% of the dissolved 

methylmercury per day at the top half meter of water (Byington et al., 2005). Extrapolating the 

methylmercury photodegradation rate of 2.5 g/day from the 2008 CALFED studies, 

Delta Methylmercury TMDL Report 125 April 2010 

 
photodegradation could account for about 30% of the 7.6 g/day loss rate illustrated in 

Figure 6.12. As described in the draft Basin Plan Amendment staff report, staff recommends 

that a control program review take place after additional Delta-specific studies are completed, 

during which the TMDL source analysis can be updated. 

The methylmercury budget in Figure 6.12 was created using data collected in a relatively dry 

period. After development and scientific peer review of the TMDL source analysis were 

completed, additional CalFed-funded studies of methylmercury in the Delta were completed. 

These studies added to our knowledge of methylmercury loads from various sources during a 

wetter period, quantified losses through photodegradation and particle deposition, and 

estimated methylmercury loads in several tidal and non-tidal wetlands (Stephenson et al., 

2008). Staff will use data from the recent CALFED studies and other studies to revise the 

methylmercury source analyses for each Delta subarea as part of the program review at the end 

of the first phase of Delta TMDL implementation. Although some methylmercury load estimates 

may change with incorporation of data from the 2008 CALFED reports, the first implementation 

activities (methylmercury control studies and total mercury reductions) proposed for the control 

program (see Chapter 4 in the draft Basin Plan Amendment staff report) would not change. 

Stakeholders participating in Stakeholder Group meetings in 2009 accepted this approach to 

using data that became available after the TMDL was developed. 

Stephenson, Foe, and colleagues developed a revised methylmercury budget for the Delta, 

based on Figure 6.12 (Foe et al., 2008). In their revised budget, tributaries provided a greater 

percentage of the methylmercury loads and wetlands and open water provided lower 

percentages than shown in Figure 6.12. The recent CALFED data were collected in a period of 

greater runoff and flows, so it is not surprising that tributary loads are larger and provide a 

greater proportion of total loading to the Delta. Other important differences between the TMDL 

budget in Figure 6.12 and the 2008 CALFED study budget include:36

• In the TMDL, the Yolo Bypass is part of the TMDL area, so its methylmercury loads are 

part of the within Delta/Yolo Bypass calculations. In the 2008 CALFED study budget, 

the Yolo Bypass is treated as a tributary to the Delta (that is, the tributary area is defined 

to be upstream of Prospect Slough), which has a substantial effect on the CalFed mass 

budget for a couple reasons: 

 The 2008 CalFed study found that in situ methylmercury production within the 

Yolo Bypass averaged 40% of the methylmercury loading to the Delta from the 

entire Sacramento Basin when the bypass was inundated (Stephenson et al., 

2008). As a result, considering this area to be “tributary” versus “within 

Delta/Yolo Bypass” causes a substantial increase in the tributary input load. 

 Nearly half of all wetlands in the Delta/Yolo Bypass are in the Yolo Bypass 

(see Figure 6.4 and Table 6.4). Classifying the Yolo Bypass (and its wetlands) 

as a tributary area causes a substantial reduction in loading attributed to withinDelta wetlands. 

 

36 Differences were identified by review of the 2008 study reports and through personal communications in 2008 

between Michelle Wood (Environmental Scientist, Central Valley Water Board) and several of the study authors: 

Chris Foe (Environmental Scientist, Central Valley Water Board), Wes Heim (Research Associate, Moss Landing 

Marine Laboratories), and Mark Stephenson (Director, Marine Pollution Studies, California Department of Fish and 

Game, Moss Landing Marine Laboratories). 

Delta Methylmercury TMDL Report 126 April 2010 

 
• The 2008 CALFED studies produced separate methylmercury flux rates for tidal, nontidal seasonal, and non-tidal permanent wetlands. All of the newer flux rates estimated 

by the recent CalFed studies are lower than the flux rate determined from the initial 

Twitchell Island study data used in the TMDL wetland load calculations. 

• The 2008 CALFED budget authors did not include non-tidal seasonal wetland acreage in 

their calculations. More than 30% of wetlands in the Delta downstream of Prospect 

Slough are non-tidal seasonal wetlands (USFWS, 2006). As a result, not including nontidal seasonal wetland acreage reduced the load attributed to within-Delta wetlands. 

• The methylmercury flux rate from open water in the 2008 CALFED budget is about half 

of the rate used in the TMDL budget. The TMDL budget is based on measurements 

taken in test chambers placed on Delta sediment (see section 6.2.2). The 2008 

CALFED budget applies the flux rate from tidal wetlands to open water. 

• Both budgets use the same total acreage of open water. However, to estimate 

methylmercury flux from open water sediment, the 2008 CALFED budget authors 

divided the open water acreage in half to account for sandy substrate. They assumed 

that sandy substrate would produce little methylmercury. 

Key points for the methylmercury source analysis are listed after Figures 6.12 and 6.13. 

Figure 6.12: Average Daily Delta/Yolo Bypass Methylmercury Inputs and Exports. The rate of unidentified 

loss processes was determined by subtracting the sum of the inputs from the sum of the exports. 

The Delta/Yolo Bypass 

 Methylmercury 

Budget 

Municipal 

WWTPs 

0.6 

g/day 

SF Bay 

-4.7 g/day 

Ag 

Return 

Flows

0.3 

g/day 

Dredging 

-0.9 g/day 

Urban 

Runoff 

0.05 

g/day 

Atmospheric 

Dep. 

0.06 

g/day 

Open 

Water

Sediment 

Flux 

2.4 

g/day 

Wetlands

Sediment 

Flux 

2.7 

g/day 

Southern CA

-1.1 g/day 

Tributary 

Inputs 

8.2 g/day 

Photodegradation 

& Particle Settling

-7.6 g/day

Delta Methylmercury TMDL Report 127 April 2010 

 
Figure 6.13: Water Sampling Transects down the Sacramento River to Ascertain Location of 

Methylmercury Concentration Decrease. Westernmost sampling stations changed with each transect 

depending on the locations of 1 o/oo through 5 o/oo bottom salinities, which move as a function of tidal 

cycle and freshwater inflow. (Data source: Foe, 2003.) 

Delta Methylmercury TMDL Report 128 April 2010 

 
Key Points 

• Sources of methylmercury in the Delta/Yolo Bypass include tributary inflows from upstream 

watersheds and within-Delta/Yolo Bypass sources such as methylmercury flux from sediment 

in wetland and open water habitats, municipal and industrial wastewater, agricultural 

drainage, and urban runoff. During the relatively dry WY2000-2003 period, approximately 

58% of identified methylmercury loading to the Delta comes from tributary inputs while withinDelta sources account for approximately 42% of the load. 

• Losses include water exports to southern California, outflow to San Francisco Bay, removal 

of dredged sediments, photodegradation, sedimentation, and uptake by biota. . 

• The sum of WY2000-2003 water imports and exports balances within approximately 5%, and 

the sum of WY2000-2003 water imports and exports balances within approximately 1%, 

indicating that all the major water inputs and exports have been identified. In contrast, the 

methylmercury budget does not balance. A comparison of the sum of identified inputs 

(5.2 kg/yr) and exports (2.5 kg/yr) indicates that there is an additional loss term of 

approximately 50%. Data collected after the TMDL source analysis was completed indicate 

that methylmercury degradation by sunlight and settling of particle-bound methylmercury 

could account for the loss. 

Delta Methylmercury TMDL Report 129 April 2010 

 
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Delta Methylmercury TMDL Report 130 April 2010 

 
7 SOURCE ASSESSMENT – TOTAL MERCURY & SUSPENDED SEDIMENT 

Sources and losses of total mercury and suspended sediment are described in this chapter. 

The Delta mercury TMDL program addresses total mercury in addition to methylmercury 

because: 

• Methylmercury production has been found to be a function of the total mercury content of 

the sediment (Chapter 3), and decreasing total mercury loads may be an option for 

controlling methylmercury; 

• The mercury control program for the Delta must maintain compliance with the USEPA’s 

CTR criterion of 50 ng/l for total recoverable mercury for freshwater sources of drinking 

water developed for human protection; and 

• The mercury TMDL for San Francisco Bay assigns a total mercury load reduction to the 

Central Valley watershed to protect human and wildlife health in the San Francisco Bay 

(Johnson and Looker, 2004; SFBRWQCB, 2006). The San Francisco Bay mercury 

control program approved by the State Water Board requires a reduction of 110 kg/yr of 

mercury from all sources entering the Delta or in water moving past Mallard Island. 

Meeting the San Francisco Bay goal will require a quantitative understanding of mercury 

and sediment loads entering and leaving the Delta. 

Sections 7.1 and 7.2 describe mercury and suspended sediment concentrations (measured as 

total suspended solids, or TSS) for Delta sources and sinks and identify major data gaps and 

uncertainties. Input and loss loads were calculated for WY2000-2003, a relatively dry period 

corresponding to the available methylmercury data. In addition, the WY1984-2003 period was 

evaluated to determine mass balances for a more typical hydrologic period. This 20-year period 

includes a mix of wet and dry years that is statistically similar to what has occurred in the 

Sacramento Basin since accurate water records began to be collected (about 100 years). An 

assessment of mass balances during a typical distribution of wet and dry water years is critical 

because transport of sediment and mercury is a function of water velocity and volume. 

Section 7.3 presents the total mercury and suspended sediment mass budgets based on the 

input and export loads described in Sections 7.1 and 7.2. Section 7.4.1 reviews the mercury-toTSS ratio (TotHg:TSS) for each input and export site to identify areas that may be the focus of 

future remediation efforts to reduce total mercury loading. Finally, Section 7.4.2 evaluates 

compliance with the CTR. 

7.1 Total Mercury and Suspended Sediment Sources 

The following were identified as sources of total mercury and suspended sediment to the Delta: 

tributary inflows from upstream watersheds, municipal wastewater, atmospheric deposition, and 

urban runoff. Table 7.1 lists the estimated loads associated with each source for WY2000-2003 

and WY1984-2003. 

Delta Methylmercury TMDL Report 131 April 2010 

 
Table 7.1: Average Annual Total Mercury and TSS Source Loads for WY2000-2003 and WY1984-2003. 

WY2000-2003 WY1984-2003 

TotHg TSS TotHg TSS 

kg/yr 

± 95% CI 

% of All

Inputs 

Mkg/yr 

± 95% CI

% of All 

Inputs 

kg/yr 

± 95% CI

% of All 

Inputs 

Mkg/yr 

± 95% CI

% of All

Inputs 

Tributary Inputs (a, b)

Sacramento River 146 ±1 66% 689 ±7 64% 183 ±1 45% 865 ±7 40% 

Prospect Slough 37 ±1 17% 197 ±5 18% 169 ±5 42% 1,014 ±31 47% 

San Joaquin River 18 ±2 8.2% 138 ±23 13% 29 ±4 7.2% 223 ±37 10% 

Calaveras River 3.8 ±2 1.7% 15 ±21 1.4% 4.1 ±2 1.0% 16 ±23 0.7% 

Mokelumne-Cosumnes Rivers 2.8 ±0.6 1.3% 7.7 ±2 0.7% 4.6 ±1 1.1% 12 ±3 0.6% 

Ulatis Creek 2.1 ±2 1.0% 16 ±19 1.5% 2.2 ±2 0.5% 17 ±19 0.8% 

French Camp Slough 1.6 ±3 0.7% 2.3 ±2 0.2% 1.7 ±3 0.4% 2.4 ±2 0.1% 

Morrison Creek 0.79 ±0.2 0.4% 4.3 ±2 0.4% 0.83 ±0.2 0.2% 4.5 ±2 0.2% 

Marsh Creek 0.54 ±0.01 0.3% 1.1 ±11 0.1% 0.54 ±0.01 0.1% 1.1 ±11 0.1% 

Bear/Mosher Creeks 0.29 ±0.2 0.1% 2.4 ±5 0.2% 0.30 ±0.2 0.1% 2.4 ±5 0.1% 

Sum of Tributary Sources: 213 ±4 97% 1,073 ±28 99% 395 ±7 98% 2,157 ±51 >99% 

Inputs within the Delta/Yolo Bypass 

Wastewater 2.5 1.1% 2.5 0.6% 

Urban 2.3 1.1% 7.5 0.7% 2.4 0.6% 7.8 0.4% 

Atmospheric (Indirect) 1.5 0.7% 1.5 0.4% 

Atmospheric (Direct) 0.81 0.4% 0.84 0.2% 

Sum of Within-Delta Sources: 7.1 3% 7.5 1% 7.2 2% 7.8 <1% 

TOTAL INPUTS: 220 ±4 1,080 ±28 402 ±7 2,165 ±51

(a) Confidence intervals (CI) were calculated for the average annual loads for inputs with daily flow data. See Appendix I for the 

calculation methods. 

(b) Total mercury and TSS concentrations are not available for several small drainages to the Delta, including the following areas shown 

on Figure 6.1: Dixon, Upper Lindsay/Cache Slough, Manteca-Escalon, Bethany Reservoir, Antioch, and Montezuma Hills areas. 

7.1.1 Tributary Inputs 

During WY2000-2003, tributaries to the Delta contributed approximately 97% of the mercury 

and 99% of the suspended sediment (Table 7.1). The Sacramento Basin alone (Sacramento 

River at Freeport + Yolo Bypass) contributed more than 80% of all mercury and TSS loads. The 

load estimates in Table 7.1 are based on the water volumes described in Section 6.1 and 

Appendix E and concentration data collected by several agencies provided in Appendix L. 

Central Valley Water Board staff began evaluating mercury loads from the Sacramento River 

watershed and Yolo Bypass in 1994 (Foe and Croyle, 1998). From March 2000 to 

September 2001, staff conducted monthly sampling at the Delta’s four major tributary input sites 

(Foe, 2003): Sacramento River; San Joaquin River; Mokelumne River (downstream of the 

Mokelumne/Cosumnes Rivers confluence); and Prospect Slough at Toe Drain in the Yolo 

Bypass. In addition, other programs conducted periodic aqueous sampling between 1993 and 

2003 on the Sacramento River (SRWP, 2004; CMP, 2004; Stephenson et al., 2002). Central 

Valley Water Board staff resumed sampling in April 2003. Figure 6.2 shows the tributary 

Delta Methylmercury TMDL Report 132 April 2010 

 
monitoring locations. Table 7.2 and Figures I.1 through I.6 in Appendix I summarize the 

mercury and TSS data available at the time the TMDL was developed. 

Sections 7.1.1.1 through 7.1.1.3 describe the methods used to estimate the loads for the Delta’s 

tributary watersheds and identify uncertainties. Because the Sacramento Basin is the primary 

source of mercury to the Delta, Section 7.1.1.3 provides an analysis of loading from major 

upstream Sacramento River tributaries. This information may be valuable for designing followup studies to determine where to implement mercury control programs. 

7.1.1.1 Sacramento Basin Inputs to the Delta 

Sacramento Basin mercury and TSS discharges to the Delta were determined for the 

Sacramento River at Freeport and the Yolo Bypass at Prospect Slough. Mercury and TSS 

concentrations for the Sacramento River at Freeport were regressed against Freeport flow to 

determine if a relationship might exist. Both regressions were statistically significant (P< 0.01) 

indicating that it is possible to predict Sacramento River mercury and TSS concentrations from 

flow. The mercury/flow and TSS/flow equations were used to predict average annual loads. 37,38

The methods used to calculate the 95% confidence intervals are described in Appendix I. The 

average annual load for the Sacramento River was 146 kg mercury and 689 Mkg TSS for 

WY2000-2003, and 183 kg mercury and 865 Mkg TSS for WY1984-2003 (Table 7.1). 

Prospect Slough is a major channel draining the Yolo Bypass. Total mercury and TSS samples 

were collected in Prospect Slough during outgoing tides. Mercury and TSS concentrations 

observed on dates with net outflow were regressed against daily outflows at Lisbon Weir lagged 

by one day39 to determine if statistically significant correlations might exist (Section E.2.2 in 

Appendix E and Figure I.1 in Appendix I). Extremely high mercury and TSS concentrations 

were measured on 10 and 11 January 1995 (Figure I.1). These values were not included in the 

regressions because, as described in Section E.2.2, the hydrologic conditions that caused them 

appear to have occurred only once during the WY1984-2003 study period. The TotHg/flow and 

TSS/flow regressions for Prospect Slough were significant (P< 0.01, Figure I.7a and I.7b), 

indicating that the concentrations of both constituents could be predicted from flow. The 

 

37 For all tributaries with statistically significant TotHg/flow or TSS/flow relationships, the predicted concentrations 

were multiplied by daily flow volumes to estimate daily loads. The estimated daily loads were summed and then 

divided by the number of years in the study period to estimate the average annual loads for WY2000-2003. If a 

flow record had dates with missing values, the data were normalized to estimate annual loads. For example, a 

20-year record would be normalized by dividing 7305 (the number of days in the 20-year period) by the number of 

days with a recorded value in the flow record and then multiplying the resulting quotient by the calculated sum of 

loads; the result was then divided by 20 to obtain the average annual load. 38 The Delta area that drains to the 13-mile reach of the Sacramento River between Freeport (near river mile 46) and 

the I Street Bridge (the northernmost legal Delta boundary, near river mile 59) is predominantly urban and is 

encompassed by the urban load estimate described in Section 5.2.5. No attempt was made to subtract this area 

from the Sacramento River watershed load estimate. Therefore, the Sacramento River load noted in Table 7.1 

incorporates a small portion of the within-Delta urban runoff loading. 39 The estimated daily flows from Lisbon Weir on Toe Drain were lagged one day to address the approximate 

residence time of water along the ~15 miles between Lisbon Weir and Prospect Slough. During drier years, there 

may be little-to-no net outflow from the Yolo Bypass’s Toe Drain downstream of Lisbon Weir between April and 

November. (See Appendix E for a description of Yolo Bypass hydrology.) Therefore, although sampling of 

Prospect Slough took place during outgoing tides with the intent of sampling outflows from the Yolo Bypass, during 

the summer months this sampling most likely represents waters tidally-pumped northward from Cache Slough, 

rather than outflows from the Yolo Bypass north of Lisbon Weir. 

Delta Methylmercury TMDL Report 133 April 2010 

 
regressions were used to estimate annual average loads of 37 kg mercury and 197 Mkg TSS for 

WY2000-2003 and 169 kg mercury and 1,014 Mkg TSS for WY1984-2003 (Table 7.1). The 

five-fold increase in loads during the wetter WY1984-2003 years illustrates the importance of 

basing load calculations on the long-term average hydrology of the basin. 

Other studies that have evaluated mercury and sediment loads from the Sacramento Basin are 

summarized in Table 7.3. The Sacramento watershed is the major source of water, mercury, 

and sediment to the Delta. The results confirm that export from the watershed is strongly a 

function of water year type. The lowest mercury export rate occurred during the driest study 

period (94.8 kg/yr; Foe 2003), while the highest (801 kg/yr; Foe and Croyle, 1998) was during a 

very wet period. Most annual loading rates fall between 200 and 500 kg of mercury per year. 

The WY1984-2003 mercury-loading rate of 349±7 kg/yr is midway between these values. The 

most comparable study is likely that of LWA (2002), which estimated an export rate of 306 kg/yr 

of mercury for another relatively similar 20-year hydrologic period. The difference between the 

two 20-year periods, while statistically significant, is only about 10%. Interestingly, the 

Sacramento River is the primary source of mercury to the Delta during dry years, but exports 

from the Yolo Bypass increase and become comparable to Sacramento River loads during wet 

periods. 

Sediment transport is also strongly a function of water year type (Table 7.3). The smallest 

export rate occurred during the driest period studied (568 Mkg/yr, Foe, 2003), while the highest 

rate happened during a wet year (3,900 Mkg/yr, Foe and Croyle, 1998). The WY1984-2003 

sediment export rate of 1,894 ±32 Mkg/yr is among the higher reported. The importance of the 

Yolo Bypass, like for mercury, is strongly a function of flow. The Bypass only exports a small 

amount of sediment during dry periods, but loads increase and equal or exceed those of the 

Sacramento River during wet periods. 

The sediment yield of the Sacramento Basin is reported to have declined by about 50% since 

1957 (Wright and Schoellhamer, 2004). Primary causes are believed to be the reduced supply 

of erodible material since cessation of hydraulic mining and increased trapping of sediment in 

reservoirs. Therefore, future Sacramento Basin mercury and sediment export rates may be 

different than those computed with the present rating curves. 

Delta Methylmercury TMDL Report 134 April 2010 

 
Table 7.2: Total Mercury and TSS Concentrations for Tributary Inputs 

Site (a)

# of 

Samples 

Sampling 

Begin Dat

e 

Sampling 

End Date 

Min. 

Conc. 

Ave. 

Conc. 

Median 

Conc. 

Max. 

Conc. 

TOTAL MERCURY CONCENTRATIONS (ng/l) 

Bear/Mosher Creeks (b) 4 3/15/03 2/26/04 3.55 8.08 8.70 11.36 

Calaveras River @ RR u/s West Lane (b) 4 3/15/03 2/26/04 13.23 20.53 21.34 26.22 

French Camp Slough near Airport Way 5 [4] 7/11/00 2/26/04 1.73 

[3.32] 

16.75 

[20.5] 

4.71 

[11.63] 

55.42 

[55.42] 

Marsh Creek @ Hwy 4 19 [3] 11/05/01 2/02/04 0.93 7.34 4.36 30.18 

Mokelumne River @ I-5 21 3/28/00 9/30/03 0.26 5.34 5.19 12.28 

Morrison Creek (c) 47 [15] 4/09/97 1/28/02 1.62 

[3.9] 

7.96 

[10.46] 

7.23 

[9.12] 

19.75 

[19.75] 

Prospect Slough (Yolo Bypass) (d) 28 [26] 1/10/95 9/30/03 10.58 73.22 

[30.80] 

26.70 

[25.73] 

695.6 

[92.2] 

Sacramento River @ Freeport 155 2/15/94 11/06/02 1.20 8.28 6.31 36.19 

San Joaquin River @ Vernalis 34 10/29/93 2/26/04 3.12 7.99 7.33 21.73 

Ulatis Creek near Main Prairie Rd 6 [4] 1/28/02 2/26/04 1.34 

[24.21] 

36.06 

[53.24] 

28.68 

[52.51] 

83.74 

[83.74] 

TSS CONCENTRATIONS (mg/l) 

Bear/Mosher Creeks (b) 4 3/15/03 2/26/04 15.8 65.8 24.1 199.1 

Calaveras River @ RR u/s West Lane (b) 4 3/15/03 2/26/04 32.4 82.7 55.4 187.5 

French Camp Slough near Airport Way 5 [4] 1/28/02 2/26/04 12.0 

[16.7] 

26.0 

[29.5] 

26.4 

[27.5] 

46.5 

[46.5] 

Marsh Creek @ Hwy 4 7 [2] 3/15/03 2/02/04 17.9 

[36.9] 

69.1 

[155.0] 

36.9 

[155.0] 

273.2 

[273.2] 

Mokelumne River @ I-5 23 3/28/00 9/30/03 5.8 14.5 12.0 31.0 

Morrison Creek (c) 44 [15] 4/09/97 1/28/02 6.0 

[7.0] 

39.9 

[57.0] 

27.0 

[40.5] 

140 

[140] 

Prospect Slough (Yolo Bypass) (d) 26 [24] 1/10/95 9/30/03 36.6 298.4 

[166.8] 

143.2 

[139.9] 

2300.7 

[512.7] 

Sacramento River @ Freeport 187 12/15/92 1/20/04 <0.5 38.0 26.0 368.0 

San Joaquin River @ Vernalis 29 3/28/00 2/26/04 20.0 61.1 56.0 170.8 

Ulatis Creek near Main Prairie Rd. 6 [4] 1/28/02 2/26/04 2.5 

[140.2] 

276.5 

[411.6] 

217.8 

[338.4] 

829.6 

[829.6] 

(a) Flow gage data were not available for most of the small tributary outflows to the Delta. Therefore, wet weather concentration data 

(noted in brackets) and estimated wet weather runoff (Section E.2.3 in Appendix E) were used to develop load estimates. 

(b) Only wet weather events were sampled on the Calaveras River and Bear and Mosher Creeks in Stockton. The one wet weather 

Mosher Creek sample result was combined with the Bear Creek data to estimate loads for both creeks (Appendix I). 

(c) Concentration data collected at multiple sites on lower Morrison Creek were compiled to develop load estimates (Appendix I). 

(d) Sampling took place at Prospect Slough (export location of the Yolo Bypass) both when there were net outflows from tributaries to the 

Yolo Bypass and when there was no net outflow (i.e., the slough's water was dominated by tidal waters from the south). The regression 

analysis focuses only on the conditions when there was net outflow from the Yolo Bypass. The above values do not include data 

collected when there was no net outflow. The values in parentheses are from calculations without the two very high values shown in 

Figure I.1. The regression is between total mercury concentrations observed at Prospect Slough (not including the two very high 

values shown in Figure I.1) and total export flows for the previous day estimated for Lisbon Weir, approximately 15 miles north of the 

Prospect Slough sampling station. The previous day's flow values were used to address the approximate residence time of the water 

as it travels through the Yolo Bypass to the export location where samples were collected. 

Delta Methylmercury TMDL Report 135 April 2010 

 
Table 7.3: Comparison of Load Estimates for Sacramento Basin Discharges to the Delta 

Study Sampling Location Period

Average 

Sacramento 

Valley 

Water Year 

Hydrologic 

Index (a)

Average 

Annual 

TotHg Load 

[± 95 CI] (kg) 

Average 

Annual 

TSS Load

[95% CI]

(Mkg)

 Sacramento River 

WY2000-2003 7.3 146 ± 1 689 ± 7 Delta Mercury TMDL (b) Freeport 

WY1984-2003 7.8 183 ± 1 865 ± 7 

Foe and Croyle (1998) Greene’s Landing May 1994- April 1995 12.9 426 1,400 

Foe (2003) Greene’s Landing WY2001 (c) 5.8 91 526 

LWA (2002) Freeport WY1980-1999 8.5 189 ± 2 na 

Wright & Schoellhamer (2005) Freeport WY1999-2002 7.7 na 1,100 ± 170 

Louie and others (2008) Freeport WY1984-2003 7.8 183 ± 2 959 ± 6 

 Yolo Bypass 

WY2000-2003 7.3 37 ± 1 197 ± 5 Delta Mercury TMDL Prospect Slough 

WY1984-2003 7.8 169 ± 5 1,014 ± 31 

Foe and Croyle (1998) Prospect Slough May 1994- April 1995 12.9 375 2,500 

Foe (2003) Prospect Slough WY2001 (c) 5.8 3.8 42 

LWA (2002) Woodland WY1980-1999 8.5 118 ± 17 na 

Wright & Schoellhamer (2005) Woodland WY1999-2002 7.7 na 310 ± 130 

Louie and others (2008) Prospect Slough WY1984-2003 7.8 168 ± 4 1,107 ± 25 

 Sacramento Basin Total (Sacramento River + Yolo Bypass)

WY2000-2003 7.3 183 ± 1 886 ± 9 Delta Mercury TMDL 

WY1984-2003 7.8 352 ± 5 1879 ±31 

Foe and Croyle (1998) May 1994- April 1995 12.9 801 3,900 

Foe (2003) WY2001 (c) 5.8 94.8 568 

LWA (2002) WY1980-1999 8.5 306 na 

Wright & Schoellhamer (2005) WY1999-2002 7.7 na 1,410 ± 300 

Louie and others (2008) WY1984-2003 7.8 351 2,066 

WY1997 10.8 487 na 

WY1998 13.3 506 na Domagalski (2001) (d)

3 winter seasons, 20 December to 20 March 

WY1999 9.8 169 na 

(a) Source: DWR, 2006 (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST). DWR calculated a hydrologic index for the Sacramento

Valley (Section E.1 in Appendix E). “Normal” hydrologic conditions for the Sacramento Valley are represented by an index value

of 7.8, “wet” ≥9.2, “dry” 5.4 to 6.5, and “critical dry” ≤5.4. Figure E.1 in Appendix E illustrates the indices for each water year for 

the period of record. 

(b) See Appendix I for the methods used to estimate the 95% confidence intervals (CI) for the TMDL load estimates. 

(c) Foe’s 2003 CALFED study estimated monthly total mercury and TSS loads for March 2000 through September 2001, but did not 

include load estimates for November 2000. November total mercury and TSS loads for WY2001 were estimated by averaging the 

loads for October and December 2000. 

(d) Domagalski (2001) reported winter mercury loads from the Sacramento Basin for WY1997 through 1999 based on data collected 

at Sacramento River at Freeport and Yolo Bypass at Interstate 80 (upstream of Putah Creek inputs), but did not report individual 

loads for the Sacramento River and Yolo Bypass. 

Delta Methylmercury TMDL Report 136 April 2010 

 
7.1.1.2 Other Tributary Inputs to the Delta 

The TotHg/flow and TSS/flow regressions for the Mokelumne-Cosumnes and San Joaquin 

Rivers were not significant (P > 0.05). Therefore, average mercury and TSS concentrations 

(Table 7.2) were multiplied by average annual water volumes for WY2000-2003 and WY1984-

2003 (Table 6.1) to estimate an average annual load. The Mokelumne River has an estimated 

average annual load of 3 kg mercury and 8 Mkg TSS for WY2000-2003 and 5 kg mercury and 

12 Mkg TSS for WY1984-2003 (Table 7.1). Similarly, the San Joaquin River has an average 

annual load of 18 kg mercury and 138 Mkg TSS and 29 kg mercury and 223 Mkg TSS, for 

WY2000-2003 and WY1984-2003, respectively. 

Several other studies have estimated mercury and sediment loads from the San Joaquin and 

Mokelumne-Cosumnes watersheds (Table 7.4). The studies confirm that mercury loads from 

both basins are much smaller than from the Sacramento Basin (Table 7.3). Annual mercury 

loads for the San Joaquin reported at the time the TMDL was developed ranged from 16 to 

29 kg/yr. The WY1984-2003 mercury load is 29 ±4 kg/yr. This value is statistically similar to 

20-year loads calculated by LWA (2002) and Louie and others (2008) of 26 kg/yr and 

28.3 ±3.0 kg/yr, respectively. Louie and others 2008 CalFed study completed since the TMDL 

was developed incorporated additional data collected during wet periods; inclusion of more data 

did not substantially change the load estimate for the San Joaquin River. 

The TMDL’s WY1984-2003 load estimate for the Mokelumne River downstream of its 

confluence with the Cosumnes River is based on data available at the time the TMDL was 

developed and is 5 ±1 kg/yr. The WY1980-1999 LWA (2002) estimate is 3 kg/yr for the 

Mokelumne River downstream of the Cosumnes River confluence. The recent CalFed study 

that incorporated additional data collected during wet periods (Louie et al., 2008) estimated 20-

year average annual loads of 1.8 ±0.08 kg/yr for the Mokelumne River and 12.4 ±0.8 kg/yr for 

the Cosumnes River, upstream of their confluence. 

Sediment export rates (Table 7.4) are also much smaller for both the San Joaquin and 

Mokelumne-Cosumnes systems than for the Sacramento Basin (Table 7.3). The TMDL’s export 

rates for the San Joaquin varied between 110 and 240 Mkg/yr. The Mokelumne-Cosumnes 

sediment yield is lower. The 20-year TMDL value is 12±3 Mkg/yr. The recent CalFed study that 

incorporated additional data collected during wet periods (Foe et al., 2008) estimated 20-year 

average annual loads of 8.4 ±0.2 kg/yr for the Mokelumne River and 48.0 ±3.2 kg/yr for the 

Cosumnes River, upstream of their confluence. 

Louie and others (2008) noted that, although the Cosumnes and Mokelumne Rivers have 

adjacent watersheds with similar average annual water budgets and both watersheds have 

histories of hydraulic gold mining, there are several watershed characteristics that could explain 

why the Cosumnes River discharges six times more mercury and sediment to the Delta than 

does the Mokelumne River. Louie and others (2008) identified the following: 

• The Mokelumne River has two major upstream impoundments (Camanche and Pardee 

Reservoirs), whereas the Cosumnes River has none. It is likely that some of the material 

being transported by the Mokelumne is deposited in upstream reservoirs and does not 

Delta Methylmercury TMDL Report 137 April 2010 

 
make it downstream to the Delta. Louie and others’ study did not include sampling for the 

reservoirs on the Mokelumne River. 

• The Cosumnes River is the largest river on the west-slope Sierra Nevada mountains 

without a major dam (Booth et al., 2006), allowing unimpaired downstream movement of 

storm runoff. For example, the maximum daily average flow for the Cosumnes River at 

Michigan Bar was 61,600 cfs during WY1984-2003, while the maximum daily average 

flow for the Mokelumne River at Woodbridge (below Camanche and Pardee Reservoirs) 

was only 5,240 cfs. Additionally, the return frequency of greater than 5,000 cfs for this 20-

year period is 1 in 4 years for the Mokelumne River and 1 in 86 days for the Cosumnes 

River. 

• The higher mercury and sediment yields from the Cosumnes are likely, at least in part, 

because the transport of both constituents is a function of water velocity (Foe and Croyle, 

1998; Foe, 2003). Higher periodic flows on the Cosumnes may result in more mercury 

and suspended sediment transport. 

Mercury and TSS loads for Marsh Creek were estimated using flow at the Marsh Creek 

Brentwood gage. The Brentwood gage was not operational during WY2000. Therefore, the 

mercury and TSS loads in Table 7.1 were based on flow data for WY2001-2003. A statistically 

significant relationship was found for mercury/flow but not for TSS/flow. Mercury concentrations 

and loads were estimated using the regression, while TSS loads were computed by multiplying 

the 3-year average annual water volume by the average TSS concentration. The WY2001-2003 

annual average mercury and TSS loads were 1 kg/yr and 1 Mkg/yr, respectively. 

There are no flow gages on several small east and westside Delta tributaries: Morrison Creek, 

Bear Creek, Mosher Creek, French Camp Slough, and Ulatis Creek. Average wet season 

mercury and TSS concentrations (Table 7.2) were multiplied by estimated average annual 

rainfall runoff volumes (Table 6.1 and Section E.2.2 in Appendix E) to calculate an average 

annual load. The WY1984-2003 estimate of mercury and suspended sediment yield from the 

combination of all these small tributaries is 5 ±2 kg/yr and 26 ±13 Mkg/yr, respectively 

(Table 7.1). 

Delta Methylmercury TMDL Report 138 April 2010 

 
Table 7.4: Comparison of Loading Estimates for Other Major Delta Tributaries 

Study Period

Average 

San Joaquin Valley 

Water Year 

Hydrologic Index (a)

Average 

Annual 

TotHg Load 

[± 95% CI] (kg) 

Average 

Annual 

TSS Load 

[± 95% CI] (Mkg)

 San Joaquin River @ Vernalis 

WY2000-2003 2.7 18 ± 2 138 ± 23 Delta TMDL (b)

WY1984-2003 3.1 29 ± 4 223 ± 37 

Foe (2003) WY2001 (c) 2.2 16 110 

LWA (2002) WY1980-1999 3.5 26 na 

Wright & Schoellhamer (2005) WY1999-2002 2.9 na 210 ± 21 

Louie and others (2008) WY1984-2003 3.1 28.3 ±3 236.9 ±29 

 Mokelumne River downstream of Cosumnes River Confluence 

WY2000-2003 2.7 3 ± 1 8 ± 2 Delta TMDL 

WY1984-2003 3.1 5 ± 1 12 ± 3 

Foe (2003) WY2001 (c) 2.2 2 5 

LWA (2002) WY1980-1999 3.5 3 na 

 Eastside Tributaries (Cosumnes, Mokelumne & Calaveras Rivers & French Camp Slough)

WY2000-2003 2.7 8 ± 2 25 ± 13 Delta TMDL 

WY1984-2003 3.1 10 ± 2 30 ± 14 

Wright & Schoellhamer (2005) WY1999-2002 2.9 na 36 ± 8 

(a) Source: DWR, 2006 (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST). DWR calculated a hydrologic index for the San 

Joaquin Valley (Section E.1 in Appendix E). “Normal” hydrologic conditions for the San Joaquin Valley are represented by an 

index value of 3.1, “wet” is ≥3.8, “dry” is 2.1 to 2.5, and “critical dry” is ≤2.1. 

(b) See Appendix I for the methods used to estimate the 95% confidence intervals (CI) for the TMDL load estimates. 

(c) Foe’s 2003 CALFED study estimated monthly total mercury and TSS loads for March 2000 through September 2001, but did 

not include load estimates for November 2000. November total mercury and TSS loads for WY2001 were estimated by 

averaging the loads for October and December 2000. 

7.1.1.3 Sacramento Basin Tributary Watersheds Loads 

The Sacramento Basin accounts for about 80% of all mercury and TSS loading to the Delta 

(Table 7.1). Therefore, an evaluation was undertaken to determine the contribution of each of 

the major tributaries. The information may prove useful to help focus follow-up studies and 

implementation actions on key watersheds that contribute a disproportionate amount of 

mercury. During low flow, water in the Sacramento River at Freeport primarily originates from 

Shasta and Oroville Dams in the upper Sacramento and Feather River basins, respectively 

(Figure 7.1). In contrast, during large storms the Sacramento River at Freeport may be 

dominated by flows from the American and Feather Rivers. Storm overflow from the upper 

Sacramento River, Feather River, and Colusa Basin are routed down the Yolo Bypass. The 

Yolo Bypass also receives flows from Putah Creek and Cache Creek via the Cache Creek 

Settling Basin. The Cache Creek Settling Basin is located at the base of the Cache Creek 

watershed and currently captures about half of the sediment and mercury transported by Cache 

Creek (Foe and Croyle, 1998; CDM, 2004; Cooke et al., 2004); untrapped sediment is flushed 

into the Yolo Bypass. 

Delta Methylmercury TMDL Report 139 April 2010 

 
Four-year (WY2000-2003) and 20-year (WY1984-2003) average annual loading values were 

calculated for major tributaries to the Sacramento River. Table 7.5 summarizes the mercury 

and TSS concentration data. Table 7.6a, b, and c present watershed acreages, annual average 

export rates for water, mercury and TSS. The data were collected by the SRWP, DWR, USGS, 

CMP, and Central Valley Water Board staff (Appendix L). The water volume calculations are 

described in Appendix E. Appendix I provides time series plots of the available mercury and 

TSS data and TotHg/flow and TSS/flow regressions described in the following pages. 

Total mercury and TSS concentrations for each tributary were regressed against flow to 

determine if correlations existed (Appendix I). The TotHg/flow and TSS/flow regressions for the 

American River, Cache Creek, Colusa Basin Drain, Feather River, Putah Creek and 

Sacramento River at Colusa were all significant (P<0.05) and were used to predict 4- and 

20-year average annual loads (Table 7.6). 

No daily flow or concentration data were available for Natomas East Main Drain (NEMD). 

Concentration data collected by the SRWP, USGS, and City of Roseville were available for 

Arcade Creek near Norwood, Del Paso Heights, and Dry Creek, all within the NEMD watershed. 

Wet weather concentration data for Arcade and Dry Creeks (noted in parentheses in Table 7.5) 

and estimated wet weather runoff for the entire Natomas East Main Drain watershed 

(Appendix E) were used to develop preliminary load estimates. The Sutter Bypass watershed 

includes the areas that drain into Butte Creek south of Chico and areas that drain into the Sutter 

Bypass between the Sacramento and Feather Rivers and south of the Sutter Buttes 

(Figure 7.1). In addition, flood flows from the Sacramento River upstream of Colusa are 

diverted into Sutter Bypass through the Moulton and Colusa bypasses; flood flows from the 

Sacramento River downstream of Colusa are diverted into the Sutter Bypass through the 

Tisdale bypass; and flood flows from the Feather River flow into the Sutter Bypass. 

Floodwaters from the Sacramento River also spill at several locations into the Butte Creek basin 

and Butte Sink, which drain to Sutter Bypass. During low flow conditions, the Sutter Bypass 

drains through Sacramento Slough near Karnak into the Sacramento River less than a mile 

upstream of the Feather River confluence. During high flow, the Sacramento Slough channel is 

submerged and the Sutter Bypass has unchannelized flow directly into the Sacramento River. 

Sutter Bypass average annual water volumes and loads (Table 7.6) were estimated using flows 

from the DWR gage on Butte Slough near Meridian. The bypass at this location includes flows 

from Butte Creek and diversions from the Sacramento River made by Moulton and Colusa 

Weirs (which are upstream of the “Sacramento River above Colusa” sampling station), but not 

Tisdale Weir or other sources that discharge to the bypass downstream of Meridian. The 

WY1998-2003 flows were used to estimate long-term average mercury and TSS loads from 

Sutter Bypass, as only flows for these years are available for the Meridian gage. WY1998-2003 

represents a relatively wetter period than the WY1984-2003, hence these load estimates may 

overestimate the Sutter Bypass contribution to the Delta. 

Total mercury and TSS concentration data were available for the Sutter Bypass at Sacramento 

Slough near Karnak, about 30 miles downstream of the Meridian flow gage. The data were 

collected between February 1996 and September 2003 during a range of flow conditions, 

including when Sacramento Slough was submerged. There is a flow gage located nearby; 

however, it was operational only during the WY1996-1998 period. In addition, it was not rated 

Delta Methylmercury TMDL Report 140 April 2010 

 
Delta Methylmercury TMDL Report 141 April 2010 

 

for flows above 5,200 cfs (Figure 7.2); flows exceeded the 5,200 cfs rating curve happened for 

extended periods during each year. Therefore, the TotHg/flow and TSS/flow regressions for 

Sacramento Slough are based only on the samples collected when the Karnak gage recorded 

flows within its rating curve, most of which are low flow events. Not surprisingly, the TotHg/flow 

and TSS/flow regressions for Sacramento Slough were not statistically significant. Therefore, 

this report’s preliminary estimates of Sutter Bypass loading (25 ±4 kg/yr for the WY1984-2003; 

19 ±3 kg/yr for the WY2000-2003 period) were developed by multiplying water volumes 

recorded by the Meridian gage by the average total mercury and TSS concentrations observed 

at Karnak. This calculation does not address any uncertainty associated with using 

concentration data collected 30 miles downstream of the flow gage. The recent CalFed study 

that incorporated additional data collected during wet periods (Louie et al., 2008) estimated a 

20-year average annual load of 31.0 ±4.2 kg/yr for the Sutter Bypass, which is statistically 

similar to the 20-year average load calculated for this report. 

Four watersheds provided more than 90% of the annual average water volume of the 

Sacramento Basin during WY2000-2003 and WY1984-2003 (Table 7.6a). The watersheds are 

the Sacramento River above Colusa, Feather River, Sutter Bypass and American River. The 

4- and 20-year water budgets balance within 4 to 5% indicating that all the major water sources 

have been identified. A different grouping of four watersheds contributed about 90% of the 

annual mercury load (Table 7.6b). The watersheds are the Sacramento River above Colusa, 

Cache Creek Settling Basin, Feather River and Sutter Bypass. The sum of tributary mercury 

inputs for both the 4 and 20-year periods is greater than the load exported to the Delta 

(Table 7.6b). Mercury exports average 79 to 87% of inputs. This suggests that either tributary 

loads are overestimated or that deposition is occurring in the river channel upstream of Freeport 

and/or in the Yolo Bypass. 

The same four watersheds that contribute the majority of the mercury also export more than 

90% of the sediment (Table 7.6c). The sum of tributary inputs of sediment is greater than the 

exports to the Delta. Exports range from 55% of inputs during WY2000-2003 to 89% during 

WY1984-2003. The results suggest, like for mercury, that incoming loads are either being 

overestimated or that deposition is occurring in the Central Valley. Wright and Schoellhamer 

(2005) and Louie and other (2008) also found that the Sacramento Basin landward of Rio Vista 

was depositional. However, unlike this report, Wright and Schoellhamer (2005) concluded that 

deposition was greater in wet than in dry periods. 
Butte Slough 

 nr Meridian 

FREEPORT

Sacramento Slough nr

K k

Figure 7.1: Sacramento River Flood Control System. 

Pink lines represent levees. (Tetra Tech, Inc., 2005b; DWR, 2003) 

Delta Methylmercury TMDL Report 142 April 2010 

 
Table 7.5: Total Mercury and TSS Concentrations for Sacramento Basin Tributaries. 

Site 

# of 

Samples

Sampling 

Begin 

Date 

Sampling 

End Date

Min. 

Conc. Average 

Median 

Conc. 

Max. 

Conc. 

Total Mercury Concentrations (ng/l) 

American River @ Discovery Park 155 1/18/94 2/19/04 0.46 2.97 2.14 18.51

Cache Creek Settling Basin 26 12/23/96 2/17/04 4.07 171.89 58.24 984.60 

Colusa Basin Drain 63 1/31/95 2/18/04 1.59 11.58 6.90 75.10

Feather River near Nicolaus 67 1/31/95 2/18/04 1.49 6.90 4.43 46.19

Natomas East Main Drain (a) 56 (12) 3/5/96 12/12/02 1.06 

(9.52) 

10.87 

(27.78) 

6.88 

(20.84) 

82.99 

(82.99) 

Putah Creek @ Mace Blvd. 36 1/31/95 3/09/04 1.25 33.02 9.14 485.00 

Sacramento River above Colusa 64 3/10/95 2/17/04 0.60 12.30 4.27 105.16

Sacramento Slough near Karnak (b) 55 2/12/96 9/15/03 0.69 8.77 7.57 30.8 

TSS Concentrations (mg/l) 

American River @ Discovery Park 191 12/15/92 2/19/04 0.5 6.23 3.0 116.0

Cache Creek d/s Settling Basin 23 12/23/96 2/17/04 41.0 425.1 140.0 1,900

Colusa Basin Drain 59 2/07/96 2/18/04 21.0 128.1 101.0 487.7

Feather River near Nicolaus 70 3/11/95 2/18/04 2.0 23.1 14.5 123.0

Natomas East Main Drain (a) 30 (8) 3/5/96 3/8/02 5.0 

(16.6) 

31.3 

(43.0) 

26.0 

(34.5) 

122.0 

(96.0) 

Putah Creek @ Mace Blvd. 29 3/28/00 2/29/04 1.6 59.01 30.0 417.8

Sacramento River above Colusa 48 3/10/95 2/17/04 10.0 98.6 36.0 662.2

Sacramento Slough near Karnak (b) 54 2/12/96 9/15/03 14.8 62.6 53.0 182.0 

(a) No concentration or flow data gage data were available for Natomas East Main Drain outflows. The SRWP, USGS and 

City of Roseville collected total mercury and TSS concentration data on Arcade Creek near Norwood and Del Paso 

Heights and Dry Creek. Wet weather concentration data for Arcade Creek and Dry Creek (noted in parentheses), and 

estimated wet weather runoff for the entire Natomas East Main Drain watershed (Table 6.1 in Chapter 6 and 

Section E.2.2 in Appendix E), were used to develop preliminary load estimates. Natomas East Main Drain was recently 

renamed “Steelhead Creek”. 

(b) Sacramento Slough near Karnak is the low flow channel for Sutter Bypass. 

Delta Methylmercury TMDL Report 143 April 2010 

 
Table 7.6a: Sacramento Basin Tributaries – Acreage and Water Volumes. 

Water Volume 

(M acre-feet/yr) % All Water

Tributary Acreage 

% All 

Acreage WY2000-2003 WY1984-2003 WY2000-2003 WY1984-2003

Upstream Tributary Inputs 

American River 1,253,740 7.5% 1.9 2.5 11% 13% 

Cache Creek 724,526 4.3% 0.22 0.38 1.3% 1.9% 

Colusa Basin Drain 1,577,307 9.4% 0.67 0.66 4.0% 3.4% 

Coon Creek/Cross Canal 287,914 1.7% 0.089 0.094 0.5% 0.5% 

Feather River 3,793,179 23% 3.9 5.3 23% 27% 

Natomas East Main Drain 231,598 1.4% 0.084 0.088 0.5% 0.5% 

Putah Creek 652,762 3.9% 0.041 0.11 0.2% 0.6% 

Sacramento River @ Colusa 7,562,525 45% 8.2 8.1 49% 41% 

Sutter Bypass 682,071 4.1% 1.8 2.3 11% 12% 

Sum of Upstream Inputs: 16,765,622 100% 16.9 19.5 100% 100% 

Exports to Delta 

Yolo Bypass (Prospect Slough) - - - 1.0 2.7 6% 14% 

Sacramento River (Freeport) - - - 15.1 16.1 94% 86% 

Sum of Exports to Delta: - - - 16.1 18.8 100% 100% 

Tributary Inputs – Exports to Delta: 0.8 0.7 

Exports to Delta / Tributary Inputs: 95% 96% 

Table 7.6b: Sacramento Basin Tributaries – Total Mercury Loads.

Average Annual TotHg Load

± 95 CI (a) (kg/yr) % of TotHg Inputs Tributary

WY2000-2003 WY1984-2003 WY2000-2003 WY1984-2003 

Upstream Tributary Inputs 

American River 6.4 ±0.1 14 ±0.1 2.8% 3.4% 

Cache Creek Settling Basin 26 ±3 118 ±5 11% 30% 

Colusa Basin Drain 10 13 4.3% 3.3% 

Feather River 28 ±1 67 ±2 12% 17% 

Natomas East Main Drain 2.9 ±1 3.0 ±1 1.2% 0.8% 

Putah Creek 1.0 ±0 8.8 ±1 0.4% 2.2% 

Sacramento River @ Colusa 139 ±4 151 ±4 60% 38% 

Sutter Bypass 19 ±3 25 ±4 8.2% 6.3% 

Sum of Upstream Inputs: 232 ±6 400 ±8 100% 100% 

Exports to Delta 

Prospect Slough 37 ±1 169 ±5 20% 48% 

Sacramento River @ Freeport 146 ±1 183 ±1 80% 52% 

Sum of Exports to Delta: 183 ±1 352 ±5 100% 100% 

Trib Inputs - Exports to Delta 49 48

Exports to Delta / Trib Inputs 79% 88%

(a) Confidence intervals (CI) were calculated for the average annual total 

mercury loads for the tributary stations with daily flow gages. See 

Appendix I for the methods used to estimate the confidence intervals. 

Delta Methylmercury TMDL Report 144 April 2010 

 
Table 7.6c: Sacramento Basin Tributaries – TSS Loads.

Average Annual TSS Load 

± 95% CI (a) (MKg/yr) % of TSS Inputs Tributary 

WY2000-2003 WY1984-2003 WY2000-2003 WY1984-2003 

Upstream Tributary Inputs 

American River 13 ±0.2 52 ±0.5 0.8% 2.4% 

Cache Creek Settling Basin 68 ±6 259 ±10 4.2% 12% 

Colusa Basin Drain 117 148 7.2% 7.0% 

Feather River 98 ±3 216 ±6 6.0% 10% 

Natomas East Main Drain 4.5 ±2 4.7 ±2 0.3% 0.2% 

Putah Creek 2.2 ±0.2 16 ±1 0.1% 0.8% 

Sacramento River above Colusa 1,180 ±41 1,256 ±41 73% 59% 

Sutter Bypass 138 ±21 177 ±27 8.5% 8.3% 

Sum of Upstream Inputs: 1,621 ±48 2,129 ±49 100% 100% 

Exports to Delta 

Prospect Slough 197 ±5 1,014 ±31 22% 54% 

Sacramento River @ Freeport 689 ±7 865 ±7 78% 46% 

Sum of Exports to Delta: 886 ±9 1,879 ±31 100% 100% 

Trib Inputs - Exports to Delta 735 250

Exports to Delta / Trib Inputs 55% 88%

(a) Confidence intervals (CI) were calculated for the average annual TSS 

loads for the tributary stations with daily flow gages. See Appendix I for 

the methods used to estimate the confidence intervals. 

A. Sacramento Slough near Knights Landing

0

2,500

5,000

7,500

Oct-83 Oct-85 Oct-87 Oct-89 Oct-91 Oct-93 Oct-95 Oct-97 Oct-99 Oct-01 Oct-03

Average Daily Flow (cfs)

Gage not rated for flows above 5,200 cfs.

Sampling

Events

B. Butte Slough near Meridian 

0

50,000

100,000

150,000

Oct-83 Oct-85 Oct-87 Oct-89 Oct-91 Oct-93 Oct-95 Oct-97 Oct-99 Oct-01 Oct-03

Average Daily Flow (cfs)

Sacramento Slough

gage rating (5,200 cfs)

 Figure 7.2: Flow Data Evaluated for Sutter Bypass. 

(Note the 20-fold difference in the Y-axis flow values for these two graphs.) 

Delta Methylmercury TMDL Report 145 April 2010 

 
7.1.2 Municipal & Industrial Sources 

During the TMDL period, WY2000-2003, there were 23 NPDES-permitted municipal and 

industrial discharges to surface water in the Delta/Yolo Bypass40 (Figure 6.5). The sum of total 

mercury loads from the discharges is approximately 2.4 kg/yr, about 1% of all Delta sources 

(Table 7.1). 

Information on average flow rates for each facility was obtained from the Central Valley Water 

Board’s discharger project files, permits and the State Water Resources Control Board’s 

Surface Water Information (SWIM) database. Effluent total mercury concentration data were 

obtained from project files and dischargers’ SIP monitoring efforts.41 Table 6.5 in Chapter 6 and 

Table G.1 in Appendix G provide additional information about the facilities. Table G.1 lists the 

estimated annual mercury loads from each facility, which were obtained from the facility-specific 

average effluent concentration and average daily discharge volume multiplied by 365. 

Appendix L provides the effluent total mercury concentration data used to calculate the average 

effluent total mercury loads. It was assumed that total mercury loading from the facilities does 

not vary substantially between wet and dry years. This consideration will be re-evaluated as 

additional information becomes available. 

Of the 23 facilities in the Delta, two are power and heating/cooling facilities that use ambient 

water for cooling water: Mirant Delta LLC Contra Costa Power Plant (CA0004863) and the State 

of California Central Heating/Cooling Plant (CA0078581). Based on the comparison of the 

available intake and outfall mercury data for the Mirant Delta facility and other similar facilities 

that discharged to the Delta in years past (Table G.5 in Appendix G), such facilities may not act 

as measurable sources of mercury to the Delta. According to its NPDES permit, the Central 

Heating/Cooling Plant adds no chemicals to its supply water; however, the permits for Mirant 

Delta and other similar facilities in the tributary watersheds indicate that mercury-containing 

chemicals may be added to their cooling water and other low-volume waste streams may be 

included in their discharges (see Tables G.6 and G.7 in Appendix G). Staff recommends that 

the assumption that power and heating/cooling plants do not contribute mercury to Delta and 

upstream surface waters be re-evaluated as additional information becomes available. 

 

40 It is assumed that facility discharges contain negligible amounts of suspended solids. 41 In September 2002, the Central Valley Water Board issued a California Water Code Section 13267 order to all 

NPDES dischargers (except municipal stormwater dischargers) requiring the dischargers to collect effluent and 

receiving water samples and to have the samples analyzed for priority pollutants contained in the 

U.S. Environmental Protection Agency's California Toxics Rule and portions of the USEPA's National Toxics Rule. 

This action was directed by Section 1.2 of the Policy for Implementation of Toxics Standards for Inland Surface 

Waters, Enclosed Bays, and Estuaries of California, also known as the State Implementation Policy (SIP), which 

was adopted by the State Water Resources Control Board on 2 March 2000. The SIP monitoring requires that the 

dischargers' mercury monitoring utilize "ultra-clean" sampling and analytical methods including Method 1669 

(Sampling Ambient Water for Trace Metals at EPA Water Quality Criteria Levels, US EPA) and Method 1631 

(Mercury in Water by Oxidation, Purge and Trap, and Cold Vapor Atomic Fluorescence, US EPA). The SIP 

monitoring requires major industrial and municipal NPDES dischargers to collect monthly samples for 

metals/mercury analysis, and minor industrial and municipal NPDES dischargers to collect quarterly samples. 

Delta Methylmercury TMDL Report 146 April 2010 

 
7.1.3 Urban Runoff 

Approximately 60,000 acres in the Delta are urban, most of which are regulated by NPDES 

waste discharge requirements. Table 6.10 in Chapter 6 lists the permits that regulate urban 

runoff and their corresponding acreage. Figure 6.7 shows their locations. Urban areas not 

encompassed by a MS4 service area were grouped into a “nonpoint source” category. 

Total mercury and TSS concentration data were collected by Central Valley Water Board staff 

and the City and County of Sacramento from several urban waterways within or adjacent to the 

Delta. Figure 6.8 shows the urban areas and sampling locations, Figure H.1 in Appendix H 

illustrates the wet and dry weather concentrations by location, and Appendix L provides the 

concentration data used in Figure H.1. Data generation by analytical methods with detection 

limits less than 1 ng/l began in 1996. The total mercury concentrations ranged from a dry 

weather low of 1.06 ng/l (Arcade Creek) to a wet weather high of 1,138 ng/l (Strong Ranch 

Slough). The TSS concentrations ranged from a dry weather low of less than 3 mg/l (City of 

Sacramento Sump 111) to a wet weather high of 1,300 mg/l (Strong Ranch Slough). A visual 

inspection of the total mercury and TSS data suggests that the differences between the urban 

watersheds are not directly related to land use. Therefore, the data were averaged by wet and 

dry weather for each location (Table 7.7). The averages of these location-based wet and dry 

weather averages are assumed to represent runoff from all urban areas in or adjacent to the 

Delta. 

To estimate wet weather mercury and TSS loads, the average wet weather concentrations were 

multiplied by the runoff volumes estimated for WY2000-2003 and WY1984-2003 for each MS4 

area within the Delta. To estimate dry weather mercury and TSS loads, the dry weather 

concentrations were multiplied by the estimated dry weather urban runoff volume. Appendix E 

describes the methods used to estimate wet and dry weather urban runoff from urban areas 

within the Delta. Wet and dry weather mercury and TSS loads were summed to estimate the 

WY2000-2003 average annual loadings of 2.3 kg mercury and 7.5 Mkg/yr suspended sediment 

and WY1984-2003 average annual loadings of 2.4 kg mercury and 7.7 Mkg/yr TSS (Table 7.8). 

Urban land uses comprise a small portion of the Delta and contribute about 1% of the mercury 

load (Table 7.1). In contrast, approximately 320,000 acres of urban land – about 42% of all 

urban area within the Delta source region – are within 20 miles of the Delta boundary, about one 

day water travel time upstream. In addition, some of the urban watersheds outside the Delta 

discharge via sumps into Delta waterways. These discharges were not included in the Delta 

urban load estimate. As a result, the urban contribution to the Delta mercury load may be 

underestimated. To evaluate the potential contributions from upstream urban lands, the total 

mercury loadings from the two MS4 service areas with the greatest urban acreage immediately 

outside the Delta were estimated for the WY1984-2003 period. The sum of mercury loads from 

the Sacramento and Stockton MS4 areas may contribute more than 2% of loading to the Delta 

(Table 7.9). These loads are expected to increase as urbanization continues around the Delta. 

Delta Methylmercury TMDL Report 147 April 2010 

 
Table 7.7: Summary of Urban Runoff Total Mercury and TSS Concentrations 

Urban Watershed 

# of 

Samples Minimum Conc. Average Conc. Maximum Conc. 

TOTAL MERCURY (ng/l) 

DRY WEATHER 

Arcade Creek 37 1.06 8.07 34.80 

City of Sacramento Strong Ranch Slough 7 3.63 18.43 84.00 

City of Sacramento Sump 104 7 1.61 7.78 24.30 

City of Sacramento Sump 111 7 2.16 9.59 28.96 

Tracy Lateral to Sugar Cut Slough 1 7.92 7.92 7.92 

Average of Location Dry Weather TotHg Averages: 10.36 

WET WEATHER 

Arcade Creek 14 1.73 20.90 54.30 

City of Sacramento Strong Ranch Slough 13 20.10 188.32 1137.90 

City of Sacramento Sump 104 14 9.94 36.72 118.42 

City of Sacramento Sump 111 13 10.68 28.56 65.23 

Stockton Calaveras River Pump Station 5 14.18 26.07 49.71 

Stockton Duck Creek Pump Station 1 13.57 13.57 13.57 

Stockton Mosher Slough Pump Station 5 9.67 14.16 17.29 

Stockton Smith Canal Pump Station 4 23.17 40.97 65.87 

Tracy Drainage Basin 10 Outflow 3 8.78 12.13 16.12 

Tracy Drainage Basin 5 Outflow 3 7.02 12.59 20.67 

Tracy Lateral to Sugar Cut Slough 3 5.44 18.10 28.45 

Average of Location Wet Weather TotHg Averages: 37.46 

TSS (mg/l) 

DRY WEATHER 

Arcade Creek 28 5.0 31.7 122.0 

City of Sacramento Strong Ranch Slough 6 5.0 9.3 15.0 

City of Sacramento Sump 104 7 4.0 7.6 12.0 

City of Sacramento Sump 111 7 1.5 6.2 11.0 

Tracy Lateral to Sugar Cut Slough 1 26.5 26.5 26.5 

Average of Location Dry Weather TSS Averages: 16.26 

WET WEATHER 

Arcade Creek 12 7.0 99.5 320.0 

City of Sacramento Strong Ranch Slough 13 23.0 208.7 1300.0 

City of Sacramento Sump 104 14 31.0 104.3 270.0 

City of Sacramento Sump 111 11 15.7 92.4 340.0 

Stockton Calaveras River Pump Station 5 26.0 94.3 264.6 

Stockton Duck Creek Pump Station 1 281.3 281.3 281.3 

Stockton Mosher Slough Pump Station 5 6.0 19.6 34.0 

Stockton Smith Canal Pump Station 4 76.0 125.8 184.6 

Tracy Drainage Basin 10 Outflow 3 81.1 136.9 236.0 

Tracy Drainage Basin 5 Outflow 3 26.1 77.5 148.1 

Tracy Lateral to Sugar Cut Slough 3 6.3 153.7 342.9 

Average of Location Wet Weather TSS Averages: 126.7 

Delta Methylmercury TMDL Report 148 April 2010 

 
Table 7.8: Average Annual Total Mercury and TSS Loadings from Urban 

Areas within the Delta/Yolo Bypass

WY2000-2003 WY1984-2003 

MS4 Permittee TotHg Load

(kg/yr)

TSS Load 

(Mkg/yr)

TotHg Load

(kg/yr)

TSS Load 

(Mkg/yr)

Contra Costa County 0.60 1.9 0.62 2.0 

Lathrop 0.032 0.10 0.033 0.11 

Lodi 0.006 0.021 0.007 0.022 

Port of Stockton 0.047 0.15 0.049 0.16 

Rio Vista 0.002 0.005 0.002 0.005 

Sacramento MS4 Permit Area 0.21 0.68 0.22 0.71 

San Joaquin Co MS4 Permit Area 0.35 1.2 0.37 1.2 

Solano County 0.019 0.062 0.020 0.065 

Stockton MS4 Permit Area 0.47 1.5 0.49 1.6 

Tracy 0.21 0.69 0.22 0.72 

West Sacramento 0.21 0.68 0.21 0.71 

Yolo County 0.050 0.16 0.051 0.17 

Urban Nonpoint Source (a) 0.10 0.33 0.10 0.33 

Grand Total 2.3 7.5 2.4 7.8 

(a) Urban areas not encompassed by a MS4 service area were grouped into a “nonpoint source” 

category within each Delta subarea. 

Table 7.9: Comparison of WY1984-2003 Annual Delta Mercury and TSS 

Loads to Sacramento and Stockton Area MS4 Loads. 

MS4 Service Area (a)

Water Volume

(M acre-feet) (b) TotHg Load (kg/year) 

TSS Load 

(Mkg/yr) 

Sacramento MS4 Urban Total 0.19 7.4 24 

Stockton MS4 Urban Total 0.026 1.0 4.0 

Total Delta Inputs (c) 23 400 1,080 

Stockton & Sacramento Urban 

Runoff as % of Total Delta Inputs 1.0% 2.1% 1.3% 

(a) The Sacramento and Stockton Area MS4s are the two MS4 service areas with the greatest 

urban acreage immediately upstream of the Delta, with urban land use areas of 160,000 

and 25,000 acres, respectively. 

(b) Refer to Appendix E for urban runoff volume estimates for wet and dry weather, which were 

summed to estimate the annual average water volumes shown above. 

(c) These values represent the sum of all tributary and within-Delta total mercury and TSS 

sources shown in Table 7.1. 

Delta Methylmercury TMDL Report 149 April 2010 

 
7.1.4 Atmospheric Deposition 

Atmospheric deposition of mercury has not been measured in the Delta until very recently. 

Figure 7.3 illustrates wet deposition sampling locations in northern and central California 

available at the time the TMDL was developed, Appendix L provides the available total mercury 

concentration data, and Table 7.10 summarizes the data. Volume-weighted average total 

mercury concentrations ranged from 4.1 ng/l at Covelo to 13 ng/l at Sequoia National Park. To 

estimate wet deposition, the volume-weighted average concentration observed at the North 

Bay/Martinez station (7.4 ng/l) was used because the station is closest to, and typically upwind 

of, the Delta. Total mercury loading from precipitation on surface water in the Delta (direct 

deposition) was estimated by multiplying the average mercury concentration in North 

Bay/Martinez rainwater (Table 7.10) by the average rainfall volume to fall on Delta water 

surfaces during WY2000-2003. Loading from runoff of mercury-contaminated rain falling on 

land (indirect deposition) was estimated by multiplying the average mercury concentration in 

rainwater by the estimated runoff volume from non-urbanized land surfaces for WY2000-2003. 

Runoff from urban areas was not included because it is inherently incorporated in the estimates 

for loading from urban runoff described in Section 7.1.3. Appendix E describes the method 

used to estimate rainfall runoff volumes for the Delta. Table 7.11 lists the estimated mercury 

loads from direct and indirect wet deposition. Wet deposition (2.3 kg/yr) contributes 

approximately 1% of all mercury entering the Delta (Table 7.1). 

There are several uncertainties inherent in the estimates of direct and indirect wet atmospheric 

deposition in the Delta. For example, the concentration of mercury in rain in the Delta had not 

been measured at the time this source analysis was developed and runoff coefficients have not 

been calculated to determine how much mercury falling on land is carried into surface water. 

However, these uncertainties are unlikely to have a substantial impact on the overall mercury 

budget for the Delta (Table 7.1) because atmospheric inputs account for only about 1% of the 

total mass balance. A recently completed CalFed study (Gill, 2008b) observed volumeweighted mercury concentrations in rain of 4.2 and 3.7 ng/l at Twitchell Island (western Delta) 

and Woodland (near the Yolo Bypass), respectively, which indicate that the estimate of wet 

deposition included in Table 7.1 may be over-estimated. 

Dry mercury deposition rates were not estimated for the Delta because there was no information 

on airborne particulate mercury concentrations at the time this source analysis was developed. 

SFEI (2001) estimated that about five times more mercury is deposited on an annual basis in 

dry than in wet deposition in San Francisco Bay. If so, direct dry deposition rates in the Delta 

may be about 12 kg/yr or about 1 to 2% of the annual load. Dr. Gill (Texas A&M University) 

recently completed measuring dry mercury deposition rates in the Central Valley as part of 

CALFED project ERP-02-C06-B. At his Woodland monitoring location, Dr. Gill estimated dry 

deposition flux rates of 1.1 and 3.4 μg/m2

/yr in the winter and summer, respectively, compared 

to his wet deposition flux rates of 2.0 and 0.10 μg/m2

/yr in the winter and summer, respectively, 

which indicates that, on an annual basis, mercury loading to the Delta from dry deposition may 

be about equal to loading from wet deposition. 

In an attempt to identify local – and therefore potentially controllable – sources of mercury in 

atmospheric deposition in the Delta and its tributary watersheds, mercury loads emitted by 

facilities that report emissions to the California Air Resources Board (ARB) were reviewed. The 

Delta Methylmercury TMDL Report 150 April 2010 

 
ARB Emission Inventory Branch tracks mercury loading in air emissions in its California 

Emission Inventory Development and Reporting System database. ARB staff provided a 

database describing facilities that reported mercury emissions in 2002. Appendix J provides a 

summary of the types of facilities in each watershed and their estimated emission loads. The 

available data indicate that almost 10 kg of mercury were released in the Delta by sugar beet 

facilities, electric services, paper mills, feed preparation, and rice milling. About 113 kg of 

mercury were released in the tributary watersheds. Some facility categories appear to have 

relatively high mercury emissions compared to other types of facilities in the tributary 

watersheds: cement, concrete and paving mixture/block manufacturing facilities (51 kg); 

electrical services (19 kg); crematories (15 kg); and national security (13 kg). Emission loads in 

Appendix J are not incorporated in the mass budgets because their deposition rates are not 

known. Local air emissions of mercury warrant additional research. 

Potentially uncontrollable sources of mercury (i.e., sources outside of the United States) in 

atmospheric deposition in the Delta and its tributary watersheds are discussed in Chapter 8, 

Section 8.4.3.5. 

Table 7.10: Summary of Available Data Describing Mercury Concentrations in Wet Deposition in Northern 

and Central California. 

Study (a) Station 

Volume-Weighted 

Average TotHg 

Conc. (ng/l)

# of 

Samples Collection Period 

North Bay 7.4 14 

Central Bay 6.6 16 

San Francisco Bay 

Atmospheric Deposition Pilot 

Study (SFBADPS) (b)

South Bay (c) 9.7 29 

Aug. 1999 – Jul. 2000 

San Jose (c) 10 86 Jan. 2000 – Dec. 2003

Sequoia National Park (d) 13 5 Jul. 2003 – Dec. 2003 

National Atmospheric 

Deposition Program (NADP) 

Mercury Deposition Network 

(MDN) Covelo (e) 4.1 60 Jan. 1998 – Sep. 2000

(a) Sources: NADP MDN – Sweet, 2000; NADP, 2004. SFBADPS – SFEI, 2001. Volume weighted average total mercury 

concentrations for the South Bay, Central Bay, and North Bay sites were calculated by the SFEI authors (SFEI, 2001). Volume 

weighted average total mercury concentrations for the San Jose, Sequoia National Park, and Covelo sites were calculated by 

Central Valley Water Board staff from the NADP data provided in Appendix L. 

(b) The North Bay, Central Bay, and South Bay sites are located at Martinez, Treasure Island and Moffett Federal Airfield/NASA 

Ames Research Center near San Jose, respectively. 

(c) In addition to being part of the SFBADPS, the South Bay site also became one of the NADP MDN stations. Co-location of 

mercury wet deposition sampling under the MDN/NADP with the Pilot Study at the South Bay site began in January 2000 and 

resulted in ten replicate field precipitation samples. 

(d) Sequoia National Park is in the Sierra Nevada Mountains to the southeast of Fresno in the Tulare Basin, which is south of the 

San Joaquin Basin. 

(e) Covelo is ~150 miles north of San Francisco Bay in the Coast Range. 

Delta Methylmercury TMDL Report 151 April 2010 

 
Table 7.11: Average Annual Total Mercury Loads from Wet Deposition (a)

WY2000-2003 WY1984-2003 

Period/Deposition Type (b)

Water Volume 

(acre-feet) (c) TotHg (kg/year)

Water Volume 

(acre-feet) (c) TotHg (kg/year)

Direct Deposition 88,669 0.81 91,960 0.84 

Indirect Deposition 159,394 1.5 165,325 1.5 

TOTAL 248,063 2.3 257,284 2.3 

(a) The volume-weighted average concentration observed in the North Bay/Martinez (7.4 ng/l, Table 7.10) 

was used to estimate total mercury loading to the Delta. 

(b) Direct deposition results from mercury-contaminated rain falling on Delta/Yolo Bypass surface waters. 

Indirect deposition results from runoff of mercury-contaminated rain falling on land surfaces in the 

Delta. Runoff from urban areas was not included because it is inherently incorporated in the estimates 

for loading from urban runoff described in Section 7.1.3. 

(c) Refer to Appendix E for a description of the methods used to estimate rainfall runoff volumes. 

Space intentionally left blank. 

Delta Methylmercury TMDL Report 152 April 2010 

 
Figure 7.3: Wet Deposition Total Mercury Sampling Locations in Northern and Central California. 

Delta Methylmercury TMDL Report 153 April 2010 

 
7.1.5 Other Potential Sources 

Loading from Delta soils has not been evaluated. More than 70% of Delta lands have 

agricultural land uses and many of the urban areas in the Delta were once agricultural. Farming 

began in the Delta in 1849, about the same time that gold mining began in the Sierra Nevada 

Mountains (DWR, 1995). In 1861, the California legislature authorized the Reclamation District 

Act, which allowed drainage of Delta swampland and construction of levees; the extensive Delta 

levee system was mostly built between 1869 and 1880 (DWR, 1995). By 1852, hydraulic 

mining was the most common method for mining the placer gold deposits in the Sierra Nevada 

(Hunerlach et al., 1999) and continued until the Sawyer Decision outlawed the practice in 1884. 

Hydraulic gold mining resulted in the deposition of large amounts of silt and sand in Delta 

channels and upstream rivers (DWR, 1995). Much of these deposits may have been 

contaminated with mercury used to amalgamate gold. Therefore, some levees and Delta 

islands may have been constructed with mercury-contaminated sediment. 

Barley and other grains have historically been common rotational crops in the Delta (Weir, 

1952), and the seeds were treated with mercury-based fungicides before sowing (LWA, 2002). 

It is not known how much mercury was used in the Delta, but up to 38,000 kg of mercury may 

have been added in fungicides in the Sacramento Valley between 1921 and 1971 (LWA, 2002). 

Mercury is no longer used as an active ingredient in any pesticides (DPR, 2002). 

Mercury has been measured in six soil samples in the Delta source region, mostly from 

agricultural fields (Bradford et al., 1996). One sample was collected in the eastern Delta near 

White Slough north of Stockton (0.27 mg/kg) and five samples were collected within 10 miles of 

the Delta boundary (0.25, 0.34, and three results <0.2 mg/kg). The study authors concluded 

that there was no relationship between soil mercury levels and location and soil type. Some of 

the mercury concentrations are elevated above the proposed San Francisco Bay TMDL 

sediment objective of 0.2 mg/kg indicating that erosion in the Delta area may contribute to 

exceedances of the Bay area sediment objective. 

Space intentionally left blank. 

Delta Methylmercury TMDL Report 154 April 2010 

 
7.2 Total Mercury and TSS Losses 

The following were identified as processes contributing to mercury loss in the Delta: flow to San 

Francisco Bay, water diversions to areas south of the Delta, removal of dredged sediments, and 

evasion of elemental mercury. Table 7.12 summarizes mercury and TSS losses by type. 

Table 7.12: Average Annual Total Mercury and TSS Losses for WY2000-2003 and WY1984-2003. 

WY2000-2003 WY1984-2003 

TotHg TSS TotHg TSS 

Load 

± 95% CI 

(kg/yr) 

% of All

Losses

Load 

± 95% CI 

(Mkg/yr) 

% of All 

Losses

Load 

± 95% CI 

(kg/yr) 

% of All 

Losses 

Load 

± 95% CI 

(Mkg/yr) 

% of All

Losses

Outflow to San Francisco Bay 270 ±93 71% 930 ±283 67% 379 ±132 78% 1,309 ±398 75% 

Dredging 57 ±71 15% 349 25% 57 ±71 12% 349 19% 

Evasion 30 8% - - -- 30 6% -- -- 

State Water Project (a) 11 ±3 3% 46 ±22 3% 9 ±3 2% 38 ±18 2% 

Delta Mendota Canal (a) 11 ±1 3% 62 ±9 5% 10 ±1 2% 60 ±9 4% 

Sum of Losses 379 ±112 100% 1,387 ±271 100% 485 ±143 100% 1,756 ±381 100% 

(a) The 95% confidence intervals (CI) were calculated for the State Water Project and Delta Mendota Canal loads using the 

method described in Appendix I. 

7.2.1 Outflow to San Francisco Bay 

Estimates of mercury and sediment exports from the Delta to San Francisco Bay are critical 

components of the Delta mercury TMDL for two reasons. First, outflow to San Francisco Bay is 

the primary export from the Delta and must be accurately measured to determine whether the 

Delta is a net source or sink for mercury and sediment. Second, the San Francisco Bay 

mercury TMDL assigned the Central Valley a mercury load allocation of 330 kg/yr. The 

allocation must be met either at Mallard Island or by a 110 kg reduction in incoming mercury 

loads to the Delta (Section 2.4.2.3). 

Central Valley Water Board staff evaluated TSS and mercury levels in Central Valley outflows to 

San Francisco Bay by collecting samples at X2. Figure 6.9 in Chapter 6 illustrates a typical 

location of X2. Board staff conducted monthly mercury and TSS sampling at X2 from 

March 2000 to September 2001 (Foe, 2003) and from April 2003 to September 2003 

(Appendix L). Table 7.13 and Figures I.4a and I.4b in Appendix I summarize the available total 

mercury and TSS concentration data for X2. Total mercury concentrations at X2 averaged 

18.1 ng/l and ranged from 3.9 ng/l to 49.2 ng/l. The TSS concentrations at X2 averaged 62 mg/l 

and ranged from 27 mg/l to 168 mg/l. Net daily Delta outflow was obtained from the Dayflow 

model (Appendix E). Total mercury and TSS concentrations at X2 were regressed against 

Delta outflow to determine whether either could be predicted from flow. Neither regression was 

significant. Therefore, average mercury and TSS concentrations were multiplied by average 

annual water volume for WY2000-2003, WY1984-2003 and WY1995-2005 to estimate annual 

loads (Table 7.14). These estimates only account for advective or riverine transport and do not 

incorporate dispersive or tidal flux. Annual average mercury loads to San Francisco Bay were 

Delta Methylmercury TMDL Report 155 April 2010 

 
270, 379, and 691 kg/yr for WY2000-2003, WY1984-2003 and WY1995-2000, respectfully 

(Tables 7.12 and 7.14). 

Six studies (including this source analysis) have measured mercury and sediment loads to San 

Francisco Bay from the Delta (Table 7.14). The results are quite variable. Some of the 

variation is undoubtedly due to the fact that different studies have measured export rates in 

different hydrologic years. However, four studies estimated annual average mercury export 

rates for WY1995-2000. The values range between 270 ±91 and 691 ±240 kg/yr (Table 7.14). 

The rate developed by David and others (2009) may be the most accurate for several reasons. 

First, it incorporates estimates of tidal dispersion in their load calculations. Tidal dispersion at 

Mallard Island reduces export rates as incoming tides have a greater sediment and mercury 

concentration than outgoing ones. This reduces the net export rate and likely provides a more 

accurate estimate. Second, it measured mercury at Mallard Island. Third, it includes data 

collected during high flows. In contrast, the TMDL’s source analysis uses sediment and 

mercury concentration data collected at X2. X2 is centered at Mallard Island but moves about 

10 miles up and down the estuary depending on river outflow and tidal stage. 

X2 measurements are appropriate for predicting biotic exposure of water column organisms, 

such as pelagic fish, to methylmercury. This was the primary objective of the study used to 

develop the TMDL’s estimate. However, such measurements are undoubtedly less reliable than 

repeated water column measurements at Mallard Island for predicting mercury and sediment 

transport past the island. 

To further complicate estimates of mercury loads to San Francisco Bay, all of the Mallard Island 

load estimates are based on the assumption that the channel at Mallard Island is well mixed. 

However, the results of a recent cross-section study suggest that mercury and suspended 

sediment concentrations are not homogenous across the Mallard channel and that caution 

should be used in estimating export loads from data collected at a single point (Louie et al., 

2006). The error estimation method used by David and others (David et al., 2009) accounts for 

heterogeneity in the cross section at Mallard Island. None-the-less, it is recommended, until 

consensus is reached on 20-year export rates at Mallard Island, that compliance with the San 

Francisco mercury allocation to the Central Valley be determined by monitoring Delta inputs. 

Table 7.13: Summary of Total Mercury and TSS Concentration Data for X2 

# of Samples (a) Min. Conc. Ave. Conc. Median Conc. Max. Conc. 

TotHg (ng/l) 20 3.95 18.10 11.59 49.20 

TSS (mg/l) 20 27.0 62.41 44.50 168.0 

(a) Sampling at X2 took place between March 2000 and September 2003. 

Delta Methylmercury TMDL Report 156 April 2010 

 
Table 7.14: Estimates of Delta Exports to San Francisco Bay 

Study (a)

Sampling 

Location Period 

Average 

Water Year 

Hydrologic 

Index (b)

Average 

Annual 

Water Volume

(M acre-feet) (c)

Average 

Annual 

TotHg Load 

± 95% CI (kg) 

Average 

Annual 

TSS Load 

± 95% CI (kg)

TotHg:TSS

(mg/kg)

WY2000-2003 7.3 12 270 ±93 930 ±283 

WY1984-2003 7.8 17 379 ±132 1,309 ±398 

Delta TMDL 

Program X2 

Calculations 

X2 (d)

WY1995-2000 11.0 31 691 ±240 2,384 ±726 

0.29 

Foe (2003) X2 WY2001 (e) 5.8 7.2 122 473 0.26 

S.F. Bay TotHg 

TMDL (2004) 

Mallard 

Island WY1995-2000 11.0 31 440 ±100 1,600 ±300 0.26 ±0.08

WY1999-2003 7.8 18 97 ±33 524 ±166 0.19 

WY2000-2003 7.3 12 83 ±28 450 ±140 0.18 

WY1995-2000 11.0 31 270 ±91 1,600 ±510 0.17 

Leatherbarrow & 

others (2005), 

McKee & others 

(2006) (f)

Mallard 

Island 

WY1995-2003 9.6 24 201 ±68 1,202 ±381 0.17 

 Louie & others 

(2008) 

Mallard 

Island WY1984-2003 7.8 17 198 ±33 801 ±160 0.25 

WY2001 5.8 7.2 53 ±19 300 ±100 - 

WY2000-2003 7.3 12 89 ±32 450 ±150 - 

WY1995-2000 11.0 31 372 ±134 1,600 ±500 - 

David & others 

(2009) 

Mallard 

Island 

WY1995-2006 9.6 24 260 ±94 1,200 ±400 0.20 (g)

(a) Sources: this report; Leatherbarrow and others, 2005; Johnson and Looker, 2004; Foe (CALFED), 2003. 

(b) DWR calculated a hydrologic index for the Sacramento Valley (DWR, 2006; see Appendix E). “Normal” hydrologic conditions for the 

Sacramento Valley are represented by an index value of 7.8, “wet” is ≥9.2, “dry” is between 5.4 and 6.5, and “critical dry” is ≤5.4. 

(c) All average annual water volumes are from the Dayflow model results for Delta outflows to San Francisco Bay. 

(d) The 95% confidence intervals (CI) were calculated using the method described in Appendix I. 

(e) Foe’s 2003 CALFED study estimated monthly total mercury and TSS loads for March 2000 through September 2001, but did not include 

load estimates for November 2000. November total mercury and TSS loads for WY2001 were estimated by averaging the loads for 

October and December 2000. 

(f) Leatherbarrow and others (2005) extrapolated total mercury loads from suspended sediment flux and suspended sediment mercury 

levels by adjusting for tidal dispersion and salinity, where for conductivity < 2 mS/cm, TotHg:TSS is 0.11 mg/kg, and conductivity 

> 2 mS/cm, TotHg:TSS is 0.29 mg/kg. Central Valley Water Board staff averaged the annual mercury and sediment load estimates 

provided by Leatherbarrow and others (2005) and McKee and others (2006) for WY1995 through 2003 to estimate average annual loads 

for the periods that correspond to the San Francisco Bay mercury TMDL study period (WY1995-2000) and the Delta mercury TMDL 

WY2000-2003 study period. Volume-weighted TotHg:TSS ratios for each period were calculated by dividing the average annual mercury 

load (kg) by average annual TSS load (Mkg). 

(g) Flow-weighted average particulate concentration for WY2002-2006, the period during which the concentration data were collected. 

7.2.2 Exports South of Delta 

Water diversions to the San Joaquin Valley and southern California account for 4 to 6% of 

mercury exports from the Delta and 6 to 8% of TSS exports (Table 7.12). Delta Mendota Canal 

(DMC) and State Water Project (SWP) exports were evaluated by collecting water samples from 

the DMC canal off Byron highway (County Road J4) and from the input canal to Bethany 

Reservoir, respectively. Bethany is the first lift station on the State Water Project canal system 

and is about one mile south of Clifton Court Forebay in the Delta (Figure 6.9). 

Central Valley Water Board staff collected monthly total mercury and TSS samples from the 

DMC and SWP between March 2000 and September 2001 (Foe, 2003) and between April 2003 

and 2004 (Appendix L). Table 7.15 and Figures I.4a and I.4b in Appendix I summarize the data. 

DMC and SWP exported water volumes were obtained from the Dayflow model (Appendix E). 

Delta Methylmercury TMDL Report 157 April 2010 

 
Total mercury and TSS concentrations were regressed against daily flow at both sites to 

determine whether concentrations could be predicted from flow. The regressions were not 

significant. Therefore, average mercury and TSS concentrations were multiplied by the 

WY2000-2003 and WY1984-2003 average annual water volume to estimate loads (Table 7.12): 

11 and 10 kg/yr for WY2000-2003 and WY1984-2003, respectively, for the DMC; and 11 and 

9 kg/yr for WY2000-2003 and WY1984-2003, respectively, for the SWP. For comparison, the 

20-year average annual loads estimated by Louie and others (2008), which incorporate data for 

a variety of wet and dry years, are 11.4 ±1.7 kg/yr for the DMC and 6.6 ±2.0 kg/yr for the SWP; 

including data for wet years did not substantially change the load estimates for these exports. 

Table 7.15: Summary of Total Mercury and TSS Concentration Data for Exports 

South of the Delta 

Site # of Samples (a) Min. Conc. Ave. Conc. Median Conc. Max. Conc. 

Delta Mendota Canal 

TotHg (ng/l) 23 1.85 3.41 3.28 5.96 

TSS (mg/l) 22 9.2 20.1 18.9 36.0 

State Water Project 

TotHg (ng/l) 20 1.16 2.91 2.20 7.17 

TSS (mg/l) 20 4.4 11.9 8.2 59.0 

(a) Sampling of these exports took place between March 2000 and September 2003. 

7.2.3 Dredging 

Sediment is dredged from the Delta to maintain the design depth of ship channels and marinas. 

Dredge material is typically pumped to either disposal ponds on Delta islands or upland areas 

with monitored return-flow. Table 6.17 provides details on recent dredge projects in the Delta 

and Figure 6.9 shows their approximate location. The Sacramento and Stockton deep water 

channels have annual dredging programs; the locations dredged each year vary. Dredging 

occurs at other Delta locations when needed, when funds are available, or when special 

projects take place. Approximately 533,000 cubic yards of sediment are removed annually with 

about 199,000 cubic yards from the Sacramento Deep Water Ship Channel and about 

270,000 cubic yards from the Stockton Deep Water Channel. Other minor dredging projects, 

mostly at marinas, remove an additional 64,000 cubic yards per year. 

The amount of mercury removed annually by dredging was estimated by multiplying dredge 

volume at each project site by its average mercury concentration. Average mercury 

concentrations in the sediment for the project sites range from 0.04 to 0.41 mg/kg (dry weight). 

Two critical assumptions were made to calculate the total mercury removed from the Delta by 

dredging projects: 

• Water content of the dredged material is 100% (50% water and 50% sediment by weight) 

(USACE, 2002); and 

Delta Methylmercury TMDL Report 158 April 2010 

 
• There are about 570 kilograms of dry sediment per cubic yard of wet dredged material 

based on relative densities of water and sediment (Weast, 1981; Elert, 2002). 

The calculations indicate that annual dredging in the Delta removes about 57 kg of mercury and 

349 Mkg of sediment. This accounts for approximately 12 to 15% of all mercury exports and 

19 to 25% of all sediment exports (Table 7.12). Board staff will continue to collect dredging data 

and evaluate the annual variability of the measurements. 

7.2.4 Evasion 

The loss of elemental mercury from water surfaces can be estimated on the basis of measured 

dissolved gaseous elemental mercury (DGM) concentrations, atmospheric mercury 

concentrations, and estimated wind speeds (Conaway et al., 2003). Conaway and others 

(2003) estimated summer and winter loss rates for San Francisco Bay. The Bay has a surface 

area of approximately 1.24 x 109

 square meters (~306,400 acres) and is estimated to lose about 

190 kg/yr of mercury to the atmosphere (Johnson and Looker, 2004). To obtain an estimate of 

evasion in the Delta, it was assumed that the loss rate would be proportional to that of San 

Francisco Bay. The mercury lost from the Bay’s surface (190 kg/year) was multiplied by the 

ratio of the water surface area of the Delta to that of the Bay (0.16). The result is an evasion 

rate of about 30 kg/yr or 6 to 8% of all mercury losses. 

After this source analysis was developed, a recent CalFed study conducted measurements of 

DGM concentrations in surface waters just west of the legal Delta boundary (Mandeville Bay, 

Suisun Bay, and Honker Bay) and within the Delta (Little Break and Georgiana Slough) and 

used this information to model the air-water exchange flux of DGM, resulting in an estimated 

loss rate of 0.99 μg/m2

/yr (Gill, 2008c). There are approximately 235,778,006 m2 of open water 

area in the Delta/Yolo Bypass (Table 6.4 in Chapter 6); when this area is multiplied by 

0.99 μg/m2

/yr, the resulting loss load is 0.23 kg/yr, a substantially lower estimate than that 

calculated in the previous paragraph. 

7.3 Total Mercury & Suspended Sediment Budgets 

Delta mercury and suspended sediment assessments rely on a box model approach to 

approximate mass balances. Mass balances are useful because the difference between the 

sum of known inputs and exports is a measure of the uncertainty of the load estimates and can 

provide an indication of whether the Delta is depositional or erosional. The average annual 

water, mercury and TSS budgets for WY2000-2003 and WY1984-2003 are presented in 

Table 7.16. 

The sum of water inputs and exports balance within 5%, indicating that all the major water 

sources and losses have been identified. In contrast, the mercury and TSS budgets do not 

balance and vary substantially depending on which estimates are used to characterize Delta 

outflows to San Francisco Bay. Table 7.16 incorporates the Delta TMDL Program’s X2 and 

evasion calculations, which results in mercury and TSS budgets that indicate that exports are 

greater than imports. This would imply that the Delta is erosional. However, this conclusion 

should be viewed with caution because the export rates used in the calculation are greater than 

Delta Methylmercury TMDL Report 159 April 2010 

 
those measured by others and may be biased high.42 The Table 7.16 budget results are also in 

conflict with the conclusions of two other studies. Wright and Schoellhamer (2005) determined 

that about 65% of the sediment entering the Delta was deposited there. Louie and others 

(2008) determined that 48% and 62% of the incoming mercury and suspended sediment loads, 

respectively, were deposited in the Delta. When the X2 and evasion load estimates shown in 

Table 7.16 are replaced with David and others (2009) Mallard Island load estimates (89 kg/yr 

and 450 Mkg/yr for WY2000-2003 mercury and sediment loads, respectively; 260 kg/yr and 

1,200 Mkg/yr for WY1995-2006 mercury and sediment loads, respectively) and the updated 

evasion estimate provided in the previous section (0.23 kg/yr), the budget results are more 

comparable to the results of the Wright and Schoellhamer (2005) and Louie and others (2008) 

studies. 

 

Table 7.16: Water, Total Mercury and TSS Budgets for the Delta for WY2000-2003 and 

WY1984-2003. 

Water Volume Average Annual Load 

(M acre-feet/yr) WY2000-2003 WY1984-2003 

WY2000-2003 WY1984-2003 TotHg (kg/yr) TSS (Mkg/yr) TotHg (kg/yr) TSS (Mkg/yr)

Inputs 20.07 23.64 221 ±4 1,081 ±28 403 ±7 2,164 ±51 

Exports 18.99 23.29 377 ±112 1,387 ±271 484 ±143 1,756 ±381 

Inputs - Exports 1.08 0.35 -156 -306 -81 408 

Exports ÷ Inputs 95% 99% 170% 128% 120% 81% 

7.4 Evaluation of Suspended Sediment Mercury Concentrations & CTR Compliance 

The evaluation of mercury contamination on suspended sediment particles for each Delta input 

and export site – in tandem with the source load analyses described in Sections 7.1 and 7.2 – is 

used to identify locations for possible remediation. The recommended total mercury control 

strategy described in Chapter 8 focuses on sources that have large mercury loadings and 

suspended sediment with high mercury concentrations, the premise being that it will be more 

cost effective to focus cleanup efforts on watersheds that export large amounts of highly 

contaminated sediment. In addition, the strategy incorporates source reductions needed to 

meet and maintain compliance with the CTR throughout the Delta. 

7.4.1 Suspended Sediment Mercury Concentrations 

Table 7.17 lists mercury to TSS ratios for Delta sources and export sites calculated using three 

different methods. The three approaches provide a range of particulate mercury contamination 

fluxing past a site. First, the ratios (in mg/kg) were estimated by dividing average annual 

mercury load (kg) by average annual TSS load (Mkg). This relationship is the preferred 

approach for Delta tributaries with statistically significant mercury and TSS relationships with 

 

42 For example, if Leatherbarrow and others’ 2005 load estimates of 83 kg/yr mercury and 450 Mkg/yr TSS are 

incorporated in the WY2000-2003 budget in Table 7.16, inputs would exceed exports, implying that the Delta is 

depositional. 

Delta Methylmercury TMDL Report 160 April 2010 

 
flow because it provides a flow-weighted estimate. The ratio was also estimated from the slope 

of the regression between mercury and TSS using paired samples. The least acceptable 

method is to take the median of the mercury to TSS ratios computed from individual paired 

samples. The median value tends to overemphasize low and moderate flows (the flows 

sampled most often) and not high flow events, which transport the majority of the suspended 

sediment and mercury. All three methods slightly overestimate particulate mercury (the focus of 

the San Francisco Bay sediment goal of 0.2 mg/kg) because none subtract the dissolved 

fraction from the total mercury concentration. 

The San Francisco TMDL for mercury includes a sediment objective of 0.2 mg/kg (Johnson and 

Looker, 2004; SFBRWQCB, 2006). Mercury contamination on sediment (TotHg:TSS) in Delta 

outflow to San Francisco Bay averaged between 0.17 mg/kg and 0.30 mg/kg (Tables 7.14 

and 7.17). The lower values are from estimates of mercury and suspended sediment loads at 

Mallard Island that attempt to better address tidal dispersion from the Bay area. The higher 

values are based on measurements taken in mid channel at X2. The higher values may 

overestimate the degree of mercury contamination being exported from the Central Valley to 

San Francisco Bay. The major source of mercury and sediment to the Delta is from the 

Sacramento Basin. Suspended sediment ratios for the Sacramento River and Yolo Bypass 

range between 0.16 and 0.24 mg/kg of mercury (Table 7.17), which are more similar to the flowweighted average particulate concentration of 0.20 for WY2002-2006 calculated by David and 

others (2009) (see Table 7.14). These values are also consistent with bulk sediment 

concentrations in the Delta of 0.15 to 0.2 mg/kg determined by Slotton and others (2003) and 

Heim and others (2003). The results suggest that the contaminated sediment at X2 did not 

entirely originate from the Central Valley during the study period. 

The X2 TotHg:TSS ratios of 0.28 to 0.30 mg/kg are similar to suspended sediment mercury 

concentrations of 0.33 mg/kg in San Pablo Bay (Schoellhamer, 1996) and bulk surficial 

sediment mercury concentrations in Suisun Bay of 0.3 to 0.35 ppm (Slotton et al., 2003; Heim et 

al., 2003). Hornberger and others (1999) report that the mercury concentration of sieved 

surficial sediment (<0.64 μm) in a core from Suisun Bay was 0.30 mg/kg; however, the 

concentration increased to 0.95 mg/kg at a depth of 30 cm. The mercury enriched zone 

persisted to a depth of about 80 cm before declining to a baseline concentration of 

0.06 ±0.01 mg/kg. The increased mercury concentration at 30 cm was ascribed to deposition of 

mercury contaminated gold tailings. No current information is available on erosion rates in 

Suisun and Grizzly Bays but both embayments were eroding at the rate of 528 Mkg per year 

between 1942 and 1990 (Cappiella et al., 2001). Therefore, a hypothesis is that the elevated 

mercury contamination on suspended sediment particles at X2 is the result of continuing 

erosion from Suisun Bay and possibly San Pablo Bay. Both embayments are within the legal 

jurisdiction of the San Francisco Bay Water Board and are part of its San Francisco Bay TMDL 

for mercury. 

Urban runoff and almost all Delta inputs have mercury to TSS ratios greater than 0.2 mg/kg 

(Table 7.17). Exceptions are the San Joaquin River, Ulatis Creek, and Yolo Bypass. An 

evaluation of the tributary sources to the Sacramento River and Yolo Bypass indicates that all 

but the Sacramento River above Colusa, Sacramento Slough and Colusa Basin Drain have 

ratios greater than 0.2 mg/kg. A comparison of Table 7.5 and Table 7.17 indicates that several 

tributaries in the Sacramento Basin have high mercury to TSS ratios and large loads of mercury. 

Delta Methylmercury TMDL Report 161 April 2010 

 
Cache Creek and Feather River have high ratios and high average annual total mercury loads. 

The American River and Putah Creek also have high ratios but comparatively smaller mercury 

loads. The Feather, American, Putah and Cache watersheds have waterways that are already 

identified on the 303(d) List as mercury-impaired. Having 303(d) Listed waterways and exports 

with elevated mercury to TSS ratios makes these watersheds attractive candidates for 

remediation efforts during the initial implementation phases of the Delta and upstream mercury 

control programs. 

In contrast, the Sacramento River above Colusa and Sacramento Slough (which receives most 

of its annual flows when upper Sacramento River flood waters are diverted to Sutter Bypass) 

have mercury to TSS ratios (0.12 and 0.13 mg/kg, respectively) comparable to background 

levels but high mercury loads. This is because both are transporting large amounts of 

sediment. The 2002 LWA report noted a similar pattern in its evaluation of median mercury to 

TSS ratios for the Sacramento Basin. Suspended sediment mercury concentrations between 

0.03 and 0.19 mg/kg may result from a combination of erosion of background soils and 

atmospheric deposition from regional and global mercury sources. Therefore, the low mercury 

to TSS ratios for the upper Sacramento River watershed may indicate, unless site-specific hot 

spots are found, that very little total mercury could be removed by means other than erosion 

control. 

A recent CalFed study evaluated particulate mercury by subtracting the dissolved (filter passing) 

fraction from the total mercury concentration and developed ratios with suspended sediment 

concentration (particulate Hg:SSC) for different Central Valley watersheds to determine the 

basins exporting the most contaminated sediment and likely responsible for a disproportionate 

amount of the downstream methylmercury production (Louie et al., 2008). Although using an 

alternative method (analysis for SSC rather than TSS), the CalFed study also determined that 

the American River, Feather River, Cache Creek Settling Basin outflow, and Putah Creek have 

elevated particulate Hg:SSC ratios, and that the Cosumnes and Mokelumne Rivers upstream of 

their confluence had elevated Hg:SSC ratios, 0.28 mg/kg and 0.18 mg/kg, respectively. 

(For comparison, the total Hg:SSC values for the Cosumnes and Mokelumne Rivers calculated 

by Louie and others were 0.41 and 0.22 mg/kg, respectively.) Several watershed 

characteristics, including its high Hg:TSS ratio make the Cosumnes River, in addition to the 

before-mentioned watersheds, an attractive candidate for remediation efforts during the initial 

implementation phases of the Delta and upstream mercury control programs; these 

characteristics are discussed in Section 8.2 in Chapter 8. 

The Louie and others 2008 CalFed study also developed Hg:SSC ratios for numerous sites in 

the upper Sacramento and San Joaquin watersheds; these will be useful for evaluating potential 

sources of mercury-contaminated sediment when TMDL control programs are developed for the 

upstream watersheds during the first phase of the Delta mercury control program’s 

implementation. 

Delta Methylmercury TMDL Report 162 April 2010 

 
Table 7.17: Mercury to Suspended Sediment Ratios for Delta Inputs and Exports 

Method A (a)

TotHg Load ÷ TSS Load

# of 

TotHg/TSS 

Paired 

Samples WY2000-

2003 

WY1984-

2003 

Method B

Linear 

Regression 

Slope for Paired 

TotHg/TSS (b)

Method C

Median of 

TotHg/TSS 

Paired Sample 

Results 

DELTA INPUTS

Bear/Mosher Creeks 4 0.12 0.07 0.24 

Calaveras River 4 0.25 0.17 0.41 

French Camp Slough 4 0.70 0.63 0.30 

Marsh Creek 7 0.49 0.12 0.19 

Mokelumne River downstream of the 

Cosumnes River 20 0.37 0.37 0.42 

Morrison Creek (c) 15 0.18 0.15 0.22 

Prospect Slough (Yolo Bypass) 44 0.19 0.17 0.18 0.20 

Sacramento River (Freeport) 134 0.21 0.21 0.17 0.24 

San Joaquin River 29 0.13 0.13 0.13 0.14 

Ulatis Creek 4 0.13 0.11 0.14 

Urban Runoff (d) 128 (123) 0.31 0.18 (0.22) 0.35 

DELTA EXPORTS

Outflows to San Francisco Bay (X2) 20 0.29 0.30 0.28 

State Water Project 19 0.24 0.18 0.29 

Delta Mendota Canal 22 0.18 0.16 0.18 

Dredging (e) 8 projects 0.19 - - - 0.03 to 0.41 

TRIBUTARIES TO THE SACRAMENTO BASIN [Sacramento River + Yolo Bypass] 

American River 109 0.50 0.27 0.20 0.41 

Cache Creek Settling Basin 21 0.39 0.45 0.48 0.36 

Colusa Basin Drain 56 0.09 0.09 0.07 

Feather River 60 0.29 0.31 0.26 0.33 

Natomas East Main Drain (Arcade Ck.) 8 0.64 0.38 0.45 

Putah Creek 29 0.45 0.55 0.26 0.30 

Sacramento River above Colusa 47 0.12 0.12 0.12 0.11 

Sutter Bypass (Sacramento Slough) 52 0.14 0.13 0.13 

(a) The preferred method for each monitoring location is highlighted in gray. If total mercury concentrations and TSS 

concentrations both correlated well with daily flow at a given monitoring location, Method A was the preferred method for 

estimating suspended sediment mercury concentrations. If the available concentration data for a location were too variable 

and/or sparse to reliably estimate annual average suspended sediment concentrations, none of the values were highlighted. 

The WY1984-2003 period was evaluated only for Sacramento Basin tributaries because the other tributary loads are based 

on average concentrations, resulting in the same TotHg:TSS ratios for both periods. 

(b) Regressions between total mercury and TSS concentrations are illustrated in Appendix I. 

(c) Appendix I provides the data for each Morrison Creek sampling location. 

(d) Urban runoff samples were collected at eleven locations. Methods B and C were performed between the urban runoff total 

mercury and TSS concentration data with and without five dramatically different sample TotHg:TSS ratios observed for 

Strong Ranch Slough. 

(e) Sediment mercury concentrations in dredged material varied substantially across the Delta. The range of project-specific 

average concentrations was 0.02 to 0.77 mg/kg. The volume-weighted average mercury concentration of all the dredged 

material was approximately 0.19 mg/kg. 

Delta Methylmercury TMDL Report 163 April 2010 

 
7.4.2 Compliance with the USEPA’s CTR 

The USEPA’s California Toxic Rule mercury criterion is 0.05 μg/L (50 ng/l) total recoverable 

mercury for freshwater sources of drinking water. The CTR criterion was developed to protect 

humans from exposure to mercury in drinking water and in contaminated fish. It is enforceable 

for all waters with a municipal and domestic water supply or consumption of aquatic organisms 

beneficial use designation. This includes all subareas of the Delta. The CTR does not specify 

duration or frequency. As noted in Chapter 2, the Central Valley Water Board has previously 

employed a 30-day averaging interval with an allowable exceedance frequency of once every 

three years for protection of human health. 

Mercury samples were not collected at a sufficiently high frequency to evaluate compliance with 

a 30-day average interval. Data therefore do not exist to show whether the CTR has actually 

been exceeded. To evaluate compliance with the CTR, regression analyses of flow and 

concentration were used to estimate 30-day running averages. As described in 

Sections 7.1.1.1 through 7.1.1.3, total mercury concentrations measured in instantaneous grab 

samples at Delta and Sacramento Basin tributary locations near flow gages were regressed 

against daily flow to determine if total mercury concentrations for days with no concentration 

data could be predicted. Figures 7.4 and 7.5 illustrate the regression-based 30-day running 

averages for locations with statistically significant (P<0.01) TotHg/flow correlations. Appendix I 

provides the TotHg/flow regressions upon which the 30-day averages are based. Table 7.18 

provides a summary of the CTR compliance evaluation. 

A waterway location was considered to be in compliance if its regression-based 30-day average 

total mercury exceeded 50 ng/l no more than once in any three-year period. Some locations 

had total mercury/flow regressions that were not statistically significant; also, some locations 

with concentration data were not near a flow gage. Such locations on larger waterways 

(e.g., Mokelumne River and San Joaquin River) were considered likely to be in compliance if 

none of the grab samples had mercury concentrations that exceeded 50 ng/l. Locations on 

small tributaries that typically experience short-duration, storm-related high flow events 

(e.g., French Camp Slough and Ulatis Creek) were considered likely to be in compliance if none 

of the water samples had mercury concentrations exceeding 50 ng/l, or if the exceedances 

occurred only during peak storm flows. 

The evaluation of regression-based 30-day running average total mercury concentrations and 

available grab sample total mercury results indicates that all sampled locations within the Delta 

– except possibly Prospect Slough and Marsh Creek – are in compliance with the CTR criterion 

for total mercury. Although none of the grab samples collected from Marsh Creek near Highway 

4 exceeded 50 ng/l total mercury, the regression-based 30-day running averages indicated that 

the CTR criterion might have been exceeded during one period. However, only about three 

years of flow data were available for the Marsh Creek location; therefore, compliance with the 

CTR criterion cannot be adequately determined with available data. Marsh Creek is already 

identified on the 303(d) List as impaired by mercury. The future mercury TMDL monitoring 

program for Marsh Creek will conduct another evaluation of CTR compliance as more data 

become available and the TMDL can incorporate total mercury load reduction requirements as 

needed to comply with the CTR. 

Delta Methylmercury TMDL Report 164 April 2010 

 
Evaluation of Yolo Bypass compliance with the CTR is complicated by the variety of watersheds 

that contribute water to it during varying hydrologic regimes. During low flow conditions, the 

Yolo Bypass receives flows from coastal mountain watersheds, particularly Cache Creek and 

Putah Creek, and other agricultural and native areas that drain directly to the bypass 

(Figure 7.1). During high flow conditions on the Sacramento River, excess flows from the upper 

Sacramento River, Sutter Bypass, Feather River, Colusa Basin, and American River 

watersheds may be routed down the Yolo Bypass at Fremont Weir, Sacramento Bypass and 

Knights Landing Ridge Cut. In a typical storm event, flows from the Cache Creek Settling Basin 

and other local sources reach the Yolo Bypass first, to be followed by lower concentration inputs 

from the Colusa Basin, Sacramento River and Feather River. 

As indicated in Figure 7.4 and described in detail in Appendix E (Section E.2.2 and Figure E.3), 

the Yolo Bypass may not experience 30 days of continuous net outflow from Lisbon Weir 

upstream of Prospect Slough during dry years. In addition, storm data collected in 1995 

indicate that total mercury concentrations in Prospect Slough (the primary outflow from the 

Bypass to the Delta) peak for a very short time. To evaluate conditions within the Bypass, the 

total mercury levels in tributary inputs to the Bypass were evaluated (Figure 7.5). The 

regression-based 30-day averages of predicted total mercury concentrations in the Sacramento 

River upstream of Colusa, Putah Creek and Feather River indicate that their flows are in 

compliance with the CTR criterion. However, the regression-based 30-day running average 

total mercury concentrations in Cache Creek Settling Basin outflows indicate that Cache Creek 

flows into the Yolo Bypass are not in compliance with the CTR criterion. This implies that when 

the Bypass is dominated by flows from Cache Creek, it may not be in compliance with the CTR 

criterion. Therefore, the Yolo Bypass area downstream of the Cache Creek Settling Basin 

probably does not meet the CTR criterion. 

The Basin Plan Amendment for control of mercury in Cache Creek was adopted by the Central 

Valley Water Board in October 2005. As outlined in the Cache Creek TMDL Basin Plan 

Amendment report (Cooke and Morris, 2005), implementation actions would enable CTR 

compliance in outflows from Cache Creek. In order to meet the mercury loading allocation 

assigned to the Central Valley by the San Francisco Bay mercury TMDL control program, the 

total mercury reduction strategy described in Chapter 8 (Section 8.2) assigns a 110 kg/yr load 

reduction to tributary inputs to the Delta, a 28% load reduction compared to the current 20-year 

average input of 395 kg/yr (see Table 7.1). Initial reduction efforts should focus on watersheds 

that contribute the most mercury-contaminated sediment to the Delta and Yolo Bypass, such as 

the Cache Creek, American River, Putah Creek, Cosumnes River, and Feather River 

watersheds. These waterways, except the Cosumnes River, are already identified on the 

303(d) List as impaired by mercury. If future monitoring indicates that Cache Creek Settling 

Basin outflows to the Yolo Bypass do not comply with the CTR even after proposed total 

mercury reductions are achieved, and other reductions designed to accomplish safe fish tissue 

methylmercury levels in Cache Creek are achieved, additional reductions will be required. 

Key points for the total mercury source analysis are listed after Figures 7.4 and 7.5 and 

Table 7.18. 

Delta Methylmercury TMDL Report 165 April 2010 

 
Sacramento River @ Freeport

0

25

50

75

TotHg Conc. (ng/L)

Predicted 30-Day Running Average

Grab Sample

Sacramento River @ RM44

0

25

50

75

TotHg Conc. (ng/L)

Predicted 30-Day Running Average

Grab Sample

CTR Criterion

Sacramento River @ Greene's Landing

0

25

50

75

TotHg Conc. (ng/L)

Predicted 30-Day Running Average

Grab Sample

CTR Criterion

Marsh Creek @ Hw y 4

0

25

50

75

Oct-83 Oct-85 Oct-87 Oct-89 Oct-91 Oct-93 Oct-95 Oct-97 Oct-99 Oct-01

TotHg Conc. (ng/L)

Predicted 30-Day Running Average

Grab Sample

CTR Criterion

Prospect Slough nr Toe Drain (Outflow s from Lisbon Weir)

0

25

50

75

100

125

TotHg Conc. (ng/L)

Predicted 30-Day Running Average for Net Outflows

Grab samples collected during tide-dominated flow conditions

Grab samples collected during net Yolo Bypass outflow

CTR Criterion

1/10/95: 695.6 ng/l

1/11/95: 553.7 ng/l

Figure 7.4: Grab Sample and Regression-Based 30-Day Running Average Total Mercury Concentrations 

for Delta Locations with Statistically Significant (P<0.05) Aqueous TotHg/Flow Correlations 

Delta Methylmercury TMDL Report 166 April 2010 

 
Cache Creek Settling Basin Outflow

0

200

400

600

800

1,000 TotHg Conc. (ng/L)

P redicted 30-Day Running A verage

Grab Sample

CTR Criterion

American River

0

10

20

30

TotHg Conc. (ng/L)

P redicted 30-Day Running A verage

Grab Sample

Colusa Basin Drain

0

20

40

60

80

TotHg Conc. (ng/L)

P redicted 30-Day Running A verage

Grab Sample

CTR Criterion

Feather River nr Nicolaus

0

20

40

TotHg Conc. (ng/L)

P redicted 30-Day Running A verage

Grab Sample

CTR Criterio n

Sacramento River abv Colusa

0

25

50

75

100

125

Oct-83 Oct-85 Oct-87 Oct-89 Oct-91 Oct-93 Oct-95 Oct-97 Oct-99 Oct-01

TotHg Conc. (ng/L)

P redicted 30-Day Running A verage

Grab Sample

CTR Criterion

Putah Creek @ Mace Blvd.

0

20

40

60

80

TotHg Conc. (ng/L)

P redicted 30-Day Running A verage

Grab Sample

CTR Criterio n

3/9-10/1995:

485 & 176 ng/l

 Figure 7.5: Grab Sample and Regression-Based 30-Day Running Average Total Mercury Concentrations 

for Sacramento Basin Tributary Locations with Statistically Significant (P<0.05) 

Aqueous TotHg/Flow Correlations 

Delta Methylmercury TMDL Report 167 April 2010 

 
Table 7.18: Evaluation of CTR Compliance at Delta and Sacramento Basin Tributary Locations 

Site 

Is TotHg/Flow 

Regression 

Significant? (a)

Does Predicted 30-Day 

Average TotHg 

Concentration Ever 

Exceed the CTR 

(50 ng/l)? (a)

# of Grab 

Samples 

> 50 ng/l 

Is the Site in 

Compliance 

with CTR? 

DELTA LOCATIONS

Bear/Mosher Creeks (b) - - - - - - 0 Likely Yes 

Calaveras River @ RR u/s 

West Lane (b) - - - - - - 0 Likely Yes 

Delta Mendota Canal No - - - 0 Likely Yes 

French Camp Slough near Airport Way - - - - - - 1 Likely Yes 

Marsh Creek @ Hwy 4 Yes Once in 3 year record. 0 Possibly Not 

Mokelumne River @ I-5 No - - - 0 Likely Yes 

Morrison Creek (c) - - - - - - 0 Likely Yes 

Outflow to San Francisco Bay No - - - 0 Likely Yes 

Prospect Slough (Yolo Bypass) (d) Yes Once (d). 5 Possibly Not 

Sacramento River @ Freeport (e) Yes No. 0 Yes 

Sacramento River @ Greene's 

Landing (e) Yes No. 4 Yes 

Sacramento River @ RM44 (e) Yes No. 1 Yes 

San Joaquin River @ Vernalis No - - - 0 Likely Yes 

State Water Project No - - - 0 Likely Yes 

Ulatis Creek near Main Prairie Rd - - - - - - 2 Likely Yes 

SACRAMENTO BASIN TRIBUTARIES (f)

American River @ Discovery Park Yes No. 0 Yes 

Cache Creek d/s Settling Basin Yes In 11 of 20 years. 15 No 

Colusa Basin Drain Yes No. 2 Yes 

Feather River near Nicolaus Yes No. 0 Yes 

Natomas East Main Drain (g) - - - - - - 1 Unknown 

Putah Creek @ Mace Blvd. (h) Yes Twice, not within 3 years. 4 Likely Yes 

Sacramento River above Colusa Yes No. 4 Yes 

Sacramento Slough near Karnak (i) No - - - 0 Likely Yes 

Delta Methylmercury TMDL Report 168 April 2010 

 
Table 7.18 Footnotes: 

(a) Flow gage data were not available for most of the small tributary outflows to the Delta. All of the regressions for sampling 

locations near a flow gage were based on 20-year flow datasets except for Marsh Creek, for which only a 3-year dataset was 

available. Regressions were considered statistically significant for R2

 values with P < 0.05. Appendix I provides the regression 

plots. 

(b) Only wet weather events were sampled on the Calaveras River and Bear and Mosher Creeks in Stockton. The one wet 

weather Mosher Creek sample result was combined with the Bear Creek dataset to evaluate compliance for both creeks. 

(c) Concentration data collected at multiple sites on lower Morrison Creek were compiled to evaluate compliance. 

(d) Sampling took place at Prospect Slough (export location of the Yolo Bypass) both when there were net outflows from tributaries 

to the Yolo Bypass and when there was no net outflow (i.e., the slough's water was dominated by tidal waters from the south). 

The regression analysis focuses only on the conditions when there was net outflow from the Yolo Bypass. Available flow 

information (Appendix E) indicates that during many years, the Yolo Bypass does not have a net outflow that lasts for 30 days 

or more. 

(e) The Sacramento River sampling locations at Freeport and River Mile 44 (RM44) are upstream and downstream, respectively, 

of the outfall for the SRCSD WWTP. Greene’s Landing is about nine miles downstream of the RM44 sampling location. 

Concentration data collected at all three sites were regressed against the flow data recorded at the Freeport gage, as no other

gages are operational in this river reach. Appendix L provides the TotHg concentration data available for all three locations.

(f) Flows from the listed tributary watersheds may be diverted to the Yolo Bypass during high flow conditions via Knights Landing 

Ridge Cut, Fremont Weir and Sacramento Weir. The Coon Creek/Cross Canal watershed also contributes to the Sacramento 

River downstream of the Feather River but no aqueous TotHg data are available for its discharges. 

(g) No concentration or flow data gage data were available for Natomas East Main Drain outflows. The SRWP, USGS and City of 

Roseville collected TotHg concentration data on Arcade Creek near Norwood and Del Paso Heights and Dry Creek. It was 

assumed that this dataset characterizes NEMD outflows. 

(h) The predicted 30-day concentrations for Putah Creek are based on modeled flows (see Appendix E) estimated since the June 

2006 draft TMDL Report. Although the regression between modeled flow and concentration is statistically significant 

(P < 0.05), there is greater uncertainty in the predicted 30-day concentrations. Two grab samples collected from a storm event

in March 1995 and two grab samples from a storm event in February 2004 had TotHg concentrations greater than 50 ng/l: 

March 9 and 10, 1995: 485 and 176 ng/l; and February 18 and 25, 2004: 126 and 53 ng/l. Figure 7.5 does not illustrate grab 

samples collected after WY2003. 

(i) Sacramento Slough near Karnak is the low flow channel for Sutter Bypass. 

Key Points 

• The primary sources of total mercury in the Delta include tributary inflows from upstream 

watersheds, atmospheric deposition, urban runoff, and municipal and industrial wastewater. 

Losses include flow to San Francisco Bay, water exports to southern California, removal of 

dredged sediments and evasion. 

• The Sacramento Basin (Sacramento River + Yolo Bypass) contributed 83 to 87% of the 

mercury load to the Delta. Most of the material was transported during high flows. 

• Estimated mercury exports rates to San Francisco Bay are quite variable. This precludes 

accurate calculations of erosion/deposition rates in the Delta and assessment of compliance 

with the proposed San Francisco Bay mercury allocation to the Central Valley at 

Mallard Island. 

• The Cache Creek, Feather River, American River, Cosumnes River, and Putah Creek 

watersheds had both relatively large mercury loadings and high mercury to TSS ratios, 

making them attractive candidates for remediation efforts during the initial implementation 

phases of the Delta and upstream mercury control program. 

Delta Methylmercury TMDL Report 169 April 2010 

 
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Delta Methylmercury TMDL Report 170 April 2010 

 
8 METHYLMERCURY ALLOCATIONS, TOTAL MERCURY LIMITS 

& MARGIN OF SAFETY 

This chapter presents recommended point and nonpoint methylmercury allocations and 

watershed total mercury limits for methyl and total mercury sources to the Delta. Reductions in 

ambient water methylmercury concentrations are required to reduce methylmercury 

concentrations in fish. Reductions in total mercury loads are needed to enable water and fish 

methylmercury reductions and to comply with the USEPA’s CTR criterion for human protection 

and the San Francisco Bay mercury TMDL control program’s total mercury allocation for the 

Central Valley. Section 8.1 describes the proposed methylmercury load and waste load 

allocations for within-Delta and tributary inputs. Section 8.2 describes the proposed watershed 

total mercury limit. Sections 8.3 and 8.4 describe the associated margin of safety and interannual and seasonal variability. 

The methylmercury allocations and total mercury limits described in this chapter reflect the 

preferred implementation alternative described in Chapter 4 of the draft Basin Plan Amendment 

staff report and are designed to address the beneficial use impairment in all subareas of the 

Delta as well as in the San Francisco Bay. However, as described in the draft Basin Plan 

Amendment report, a number of alternatives are possible. The Central Valley Water Board will 

consider a variety of allocation strategies and implementation alternatives as part of the Basin 

Plan amendment process. 

8.1 Methylmercury Load Allocations 

Since the June 2006 draft TMDL and Basin Plan Amendment staff reports issued for scientific 

peer review, staff made the following changes to this section in response to comments made by 

the scientific peer reviewers and other agencies and stakeholders: 

• Developed allocations only for dischargers within the legal Delta and the Yolo Bypass 

(including the portion north of the legal Delta), versus the legal Delta and all dischargers 

within 30 miles of the legal Delta boundary. 

• Provided additional explanation of, and calculations for, the proposed methylmercury 

allocations to more directly address expected increases in source loading from predicted 

population growth and wetland restoration efforts and to acknowledge the efforts of those 

point sources whose effluent quality demonstrates good performance. 

• Changed the methylmercury allocation strategy such that all point and nonpoint sources 

have load-based (versus load- and concentration-based) allocations to allow for a greater 

range of implementation options. 

• Established percent allocations for tributary inputs based on a methylmercury 

concentration of 0.05 ng/l (rather than 0.06 ng/l, the proposed methylmercury goal for 

ambient water) to reserve assimilative capacity for methylmercury flux from sediments in 

open-water and wetland habitats and agricultural lands, and point source discharges 

within the Delta/Yolo Bypass with discharge methylmercury concentrations that exceed 

0.06 ng/l. 

Delta Methylmercury TMDL Report 171 April 2010 

 
• Re-calculated all allocations based on existing methylmercury discharge concentrations 

rounded to two decimal places and existing methylmercury loads rounded to two 

significant digits. 

• Re-organized the text to avoid redundancy with allocation strategy explanations provided 

in Chapter 4 of the draft Basin Plan Amendment staff report and to improve clarity. 

Since the February 2008 draft TMDL and Basin Plan Amendment staff reports issued for public 

review, staff made the following changes to this section in response to input from the 2008-2009 

Stakeholder Process and written stakeholder comments submitted before the April 2008 hearing 

meeting: 

• Adjusted the method for calculating the waste load allocations for NPDES facilities to 

better address regionalization efforts and population growth. 

• Updated the waste load allocations for NPDES facilities to reflect that several facilities no 

longer discharge to surface waters and that new facility discharges have begun since the 

TMDL period, WY2000-2003. 

• Added to text to clarify how the waste load allocations are applied to MS4 service areas 

and other point and nonpoint sources. 

• Adjusted the load allocations for tributary inputs and open-water habitat in all Delta 

subareas to incorporate the same percent reductions required for other point and 

nonpoint sources that discharge to those subareas (rather than setting tributary input 

allocations equal to the load calculated using a methylmercury concentration of 0.05 ng/l, 

and setting open water allocations equal to existing average annual methylmercury loads, 

as was done in the February 2008 draft report). 

• Added text to clarify how waste load and load allocations are calculated. 

8.1.1 Definition of Assimilative Capacity 

A water body’s loading capacity (assimilative capacity) represents the maximum rate of loading 

of a pollutant that the water body can assimilate without violating water quality standards. A 

TMDL typically represents the sum of all individual allocations of the water body’s assimilative 

capacity and must be less than or equal to the assimilative capacity. Allocations are divided 

among “waste load allocations” for point sources and “load allocations” for nonpoint sources 

including natural background. The TMDL is the sum of these components: 

Equation 8.1: 

 TMDL = Waste Load Allocations + Load Allocations 

For the Delta methylmercury TMDL, waste load allocations apply to discharges from existing 

and future NPDES-permitted WWTPs and MS4s within the Delta and Yolo Bypass. Load 

allocations apply to methylmercury flux from existing and future wetland and open-water 

sediments and agricultural lands and atmospheric deposition within the Delta and Yolo Bypass, 

as well as to tributary inputs to the Delta/Yolo Bypass. Natural background sources include 

atmospheric deposition, methylmercury flux from wetland and open-water sediments, and runoff 

Delta Methylmercury TMDL Report 172 April 2010 

 
from upland areas that existed prior to human-related pollution emissions such as mercurycontaminated sediment from historical mining activities in the tributary watersheds, mercury 

emissions from local and international industrial and municipal sources, and water management 

activities. Natural background sources are incorporated in the load allocations for wetlands, 

open water, and atmospheric deposition because data were not available to distinguish 

between natural background and nonpoint sources. 

A TMDL need not be stated as a daily load (Code of Federal Regulations, Title 40, §130.2[i]). 

Other measures are allowed if appropriate. The methylmercury allocations proposed in 

Table 8.4 at the end of Section 8.1.3 are expressed in terms of average annual loads because 

the adverse effects of mercury occur through long-term bioaccumulation. The allocations are 

intended to represent annual averages and account for both seasonal and long-term variability. 

The annual load and waste load allocations can be expressed in daily terms by simply dividing 

each allocation by 365.43 However, to best attain and maintain the proposed fish tissue 

objectives, staff recommends that the allocations be implemented as average annual loads. 

Methylmercury allocations were made in terms of the existing assimilative capacity of each of 

the different Delta subareas. A methylmercury TMDL must be developed for each Delta 

subarea because the sources and percent reductions needed to meet the proposed 

implementation goal are different in each subarea. The linkage analysis (Chapter 5) described 

the calculation of an implementation goal for methylmercury in ambient water that is linked to 

the fish tissue methylmercury targets. The recommended implementation goal is an annual 

average concentration of 0.06 ng/l methylmercury in unfiltered water. This goal describes the 

assimilative capacity of Delta waters in terms of concentration (Section 5.2). Central Valley 

Water Board staff anticipates that as the average concentration of methylmercury in each Delta 

subarea decreases to the safe aqueous goal, the targets for fish tissue will be attained. To 

determine necessary reductions, the existing average aqueous methylmercury levels in each 

Delta subarea were compared to the methylmercury goal (Table 8.1). 

The amount of reduction needed in each subarea is expressed as a percent of the existing 

concentration. As noted in the linkage analysis, the aqueous methylmercury goal was 

developed using water data for March to October 2000 because this was the only period for 

which there was overlap between water data and the lifespan of the fish. Table 8.1 compares 

the proposed goal to average methylmercury concentrations for March to October 2000 

(Scenario A) and for March 2000 to April 2004 (Scenario B). Scenario B is based on a much 

larger dataset and includes values for all seasons. However, the percent reductions are similar 

for both scenarios and range from 0 to 80% for the different subareas. Therefore, staff 

recommends the use of the proposed reductions listed in Scenario B for the calculation of 

assimilative capacity. 

The assimilative capacity of each subarea (Table 8.2) was determined using the proposed 

reductions listed in Scenario B in Table 8.1 (except for the Central and West Delta subareas, as 

 

43 In its November 2006 memorandum concerning appropriate time increments for TMDLs, the USEPA recommended 

that States provide written documentation regarding how the TMDL allocations can be expressed in daily terms 

(USEPA, 2006). 

Delta Methylmercury TMDL Report 173 April 2010 

 
discussed in the next paragraphs), the sum of existing annual methylmercury inputs from 

identified sources (see Table 8.4 at the end of Section 8.1.3) and the following equation: 

Equation 8.2: (using the Sacramento subarea as an example) 

 Assimilative = Existing MeHg – % Reduction Needed to * Existing MeHg 

 Capacity (g/yr) Inputs (g/yr) Meet Proposed Goal Inputs (g/yr) 

 = 2,418 g/yr – (44% * 2,418 g/yr) 

 = 1,354 g/yr 

The subareas on the eastern boundary of the Delta require substantial reductions in fish and 

aqueous methylmercury levels. In contrast, ambient methylmercury concentrations in the 

Central and West Delta subareas equal or approach the proposed aqueous methylmercury goal 

of 0.06 ng/l, resulting in the need for little-to-no reductions in methylmercury inputs to these 

subareas. The Central and West Delta subareas receive methylmercury from within-subarea 

sources, tributaries that drain directly to the subareas, and flows from upstream Delta subareas. 

The Central Delta subarea receives flows from the Sacramento, Yolo Bypass, Mokelumne, and 

San Joaquin subareas. The West Delta subarea receives flows from the Central Delta and 

Marsh Creek subareas. These within-Delta flows have not yet been quantified because 

additional data are needed for loss rates across the subareas. However, methylmercury in 

these subarea inflows are expected to decrease substantially (e.g., 40-80%) as upstream 

methylmercury and mercury management practices take place because methylmercury source 

load reductions ranging from 44 to 80% are required for the upstream subareas to achieve their 

assimilative capacities. In addition, the primary within-subarea source of methylmercury in the 

Central and West Delta subarea is flux from open-water habitat sediments (Table 8.4), which is 

expected to decrease as mercury reduction projects take place in the tributary watersheds that 

result in decreasing the mercury concentration of sediment deposited in the Central and West 

Delta subareas. Therefore, staff recommends that no reduction be required for point and 

nonpoint source methylmercury discharges within the Central and West Delta subareas. 

Section 8.1.2 describes an allocation strategy that ensures that fish and water methylmercury 

concentrations in these subareas remain in compliance with the proposed fish tissue objectives 

and methylmercury goal for water. The Central Valley Water Board can consider modification of 

the allocation strategy and the creation of new allocations (e.g., for within-Delta flows between 

subareas) during the program review proposed to take place in about seven years based on 

existing and new information that becomes available. 

The following three sections describe the strategy and calculations used to determine specific 

allocations for point and nonpoint sources listed in Table 8.4 for each of the subareas. 

Delta Methylmercury TMDL Report 174 April 2010 

 
Table 8.1: Aqueous Methylmercury Reductions Needed to Meet the Proposed Methylmercury Goal of 

0.06 ng/l. (a)

Delta Subarea 

 Central 

Delta 

Marsh 

Creek 

Mokelumne 

River 

Sacramento 

River 

San Joaquin 

River 

West 

Delta 

Yolo 

Bypass

A. Scenario Based on March to October 2000 Aqueous MeHg Data (b)

Average Aqueous MeHg 

Concentration (ng/l) 0.055 0.224 0.140 0.120 0.147 0.087 0.305 

Percent Reduction Needed to 

Meet the Proposed MeHg Goal 0% 73% 57% 50% 59% 31% 80% 

B. Scenario Based on March 2000 to April 2004 Aqueous MeHg Data (b)

Average Annual Aqueous 

MeHg Concentration (ng/l) 0.060 0.224 0.166 0.108 0.160 0.083 0.273 

Percent Reduction Needed to 

Meet the Proposed MeHg Goal 0% 73% 64% 44% 63% 28% 78% 

(a) The amount of reduction needed in each subarea is expressed as a percent of the existing methylmercury concentration. For 

example, the percent reduction needed for the Marsh Creek subarea Scenario A is calculated by: (0.244 - 0.06) / 0.244 = 73%. 

The average March to October 2000 methylmercury concentration for the Central Delta is below the proposed implementation 

goal of 0.06 ng/l. As a result, Scenario A calculations for the Central Delta result in negative numbers: A (1): (0.055 - 

0.06)/0.055 = -9%. No reduction is needed under Scenario A or B for Central Delta ambient methylmercury. 

(b) Average concentrations are based on unfiltered MeHg concentration data collected at the following locations: Delta Mendota 

Canal and State Water Project (Central Delta); Marsh Creek at Highway 4; Mokelumne River near I-5; Sacramento River at 

Freeport, RM44 and Greene’s Landing; San Joaquin River near Vernalis; outflow to San Francisco Bay measured at X2, 

usually near Mallard Island (West Delta); and Prospect Slough near Toe Drain (Yolo Bypass). The values for the Central 

Delta, Mokelumne River, Sacramento River, San Joaquin and West Delta subareas are described in Section 5.1 and Table 5.1 

in Chapter 5 and are based on monthly average concentrations so that the average concentrations for each study period are 

not influenced by the unequal number of samples collected in each month. The Yolo Bypass average concentrations also are 

based on monthly average concentrations. The sampling frequency on Marsh Creek was inadequate to develop averages for 

each study period, much less to pool data by month; therefore, the average of all available concentration data was used in 

both scenarios. The Yolo Bypass and Marsh Creek data are described in Chapter 6, Section 6.2.1 and Table 6.3. It was 

assumed that the sampling locations are representative of the subareas in which they occur. 

Table 8.2: Assimilative Capacity Calculations for Each Delta Subarea. 

Delta Subarea 

Existing Average 

Annual MeHg 

Conc. (a) (ng/l)

% Reduction Needed 

to Achieve Proposed 

Goal of 0.06 ng/l (a)

Existing Annual MeHg 

Load from Identified 

Sources (b) (g/yr)

Assimilative 

Capacity 

(g/yr)

Central Delta 0.060 0% 668 668 

Marsh Creek 0.224 73% 6.14 1.66 

Mokelumne River 0.166 64% 146 52.6 

Sacramento River 0.108 44% 2,475 1,385 

San Joaquin River 0.160 63% 528 195 

West Delta 0.083 0% 330 330 

Yolo Bypass [North & South] 0.273 78% 1,068 235 

(a) No percent reductions are proposed for the Central and West Delta subareas because their fish tissue and aqueous 

methylmercury levels either currently achieve or are expected to achieve safe levels when actions are implemented to reduce 

upstream aqueous methylmercury levels. Proposed reductions for other subareas are from Table 8.1 Scenario B. 

(b) "Existing Annual MeHg Load" represents the sum of all identified inputs to each subarea (Chapter 6 and Table 8.4). 

Delta Methylmercury TMDL Report 175 April 2010 

 
8.1.2 Allocation Strategy 

Table 8.4 at the end of Section 8.1.4 lists waste load and load allocations for each point and 

nonpoint methylmercury input by subarea and reflects the preferred implementation alternative 

and resulting allocation strategy described in Chapter 4 of the draft Basin Plan Amendment staff 

report. This section summarizes key elements of the preferred allocation strategy developed in 

the draft Basin Plan Amendment staff report. Section 8.1.3 provides detailed explanations of 

calculation methods for NPDES facility waste load allocations. Section 8.1.4 describes the 

equations used to calculate the load and waste load allocations for nonpoint and point sources 

in each Delta subarea. 

The available science is adequate to establish individual allocations for point sources in the 

Delta/Yolo Bypass and tributary inputs to the Delta/Yolo Bypass, and general (subarea) 

methylmercury allocations for nonpoint sources within the Delta/Yolo Bypass. The preferred 

allocation strategy specifies the following: 

• Atmospheric deposition and discharges from urban areas outside of MS4 service areas in 

all Delta subareas have load allocations set at their existing average annual 

methylmercury loads. 

• All point and nonpoint sources in the Central and West Delta subareas have waste load 

and load allocations set at their existing average annual methylmercury loads to ensure 

that compliance with the fish tissue objectives is maintained. 

• Waste load and load allocations integrate expected expansions to existing sources and 

new sources. 

• Waste load allocations acknowledge the efforts of those point sources whose effluent 

quality demonstrates good performance, and require improvement by other dischargers. 

Anticipated population growth, regional water management changes, and wetland restoration 

efforts could result in increases in methylmercury loading to the Delta. For example, increasing 

populations will result in increasing total mercury and methylmercury discharges from municipal 

WWTPs and urban runoff. The California Department of Finance predicts that populations in 

the Delta/Yolo Bypass counties44 will increase 76% to 213% by 2050 (CDOF, 2007), with an 

average increase of about 120%. (For more discussion on potential regional changes, see 

Section 8.4.3, “Regional and Global Change”.) 

The allocations for each existing source apply to the sum of its existing discharge and any 

expansion to its discharge in the future, with the exceptions noted in Section 8.1.3. The 

recommended open-water and wetland methylmercury allocations apply to all wetlands and 

open-water habitat acreage in each Delta subarea, including current wetlands and future 

wetland restoration projects. The subarea load allocations for agricultural lands apply to the net 

difference between methylmercury loads discharged by agricultural lands during the irrigation 

season and methylmercury loads in irrigation water applied to the agricultural lands. Similarly, 

the subarea load allocations for wetlands apply to the net difference between methylmercury 

 

44 The CDOF predicts the following population increases by 2050: Contra Costa County - 89%, 

Sacramento County - 76%, San Joaquin County - 213%, Solano County - 105%, and Yolo County - 93% 

(CDOF, 2007). 

Delta Methylmercury TMDL Report 176 April 2010 

 
loads discharged by wetlands and methylmercury loads in the wetlands’ source water (surface 

water, groundwater and precipitation). The load allocations for agricultural lands, wetlands, and 

open-water habitat do not include methylmercury loading from atmospheric wet deposition. 

The MS4 waste load allocations apply to all urban land use areas within MS4 service areas 

within each Delta subarea and similarly address loading from current and future urban areas 

within the MS4 service areas, including but not limited to Caltrans facilities and rights-of-way 

(NPDES No. CAS000003), public facilities, properties proximate to banks of waterways, 

industrial facilities, and construction sites. The MS4 waste load allocations do not apply to nonurban land uses within MS4 service areas. The load allocations for agricultural lands, wetlands, 

and open-water habitat include methylmercury loading from agricultural lands, wetlands, and 

open water habitat within MS4 service areas. Some MS4s service areas span multiple Delta 

subareas and therefore have multiple subarea allocations and are listed more than once. The 

waste load allocations do not apply to urban land within the MS4 service areas that are outside 

of the legal Delta and Yolo Bypass boundaries. The Contra Costa County MS4 discharges to 

both the Delta and San Francisco Bay; the subarea allocations in Table 8.4 apply only to the 

portions of the MS4 service area that discharge to the Delta within the Central Valley Water 

Quality Control Board’s jurisdiction. The waste load allocations for urban land within MS4 

service areas include methylmercury loading from atmospheric wet deposition, consistent with 

how allocations were developed for the recently-adopted San Francisco Bay and Guadalupe 

River Watershed mercury TMDLs (Johnson and Looker, 2004; SFBRWQCB, 2008). Urban 

areas were not included in the atmospheric wet deposition load calculations to avoid doublecounting. Urban areas not encompassed by a MS4 service area were grouped into a “urban 

runoff (nonpoint source)” allocation for each Delta subarea, consistent with USEPA’s 

requirements and guidance for establishing waste load allocations for storm water sources 

(USEPA, 2002). 

Staff recommends that methylmercury waste load allocations for NPDES facilities apply to their 

annual (calendar year) discharge methylmercury loads with one exception. Staff recommends 

that assessment of compliance with the waste load allocation for the Oakwood Lake Subdivision 

Mining Reclamation discharges (CA0082783) be assessed as a five-year average annual 

methylmercury load because its discharges result from flood-control pumping, which can 

fluctuate with short-term and long-term precipitation patterns. Similarly, annual loads for 

tributary inputs, urban discharges, open-water habitat, and atmospheric deposition are based 

on water years 2000 through 2003, a relative dry period, and expected to fluctuate with rainfall 

and river flow conditions and other environmental factors. As a result, staff recommends that 

assessment of compliance with load allocations for the tributary inputs, urban areas outside of 

MS4 service areas, open-water habitat, and atmospheric deposition, and waste load allocations 

for the MS4s, be based on five-year average annual loads. As described in the draft Basin Plan 

Amendment staff report, staff recommends that a Delta mercury control program review take 

place in about seven years, during which the allocations can be revised to include available wet 

year data and other new information. 

Methylmercury data were not available for inputs to the Yolo Bypass from Willow Slough and 

runoff from the Dixon area. The average methylmercury concentration for Ulatis Creek was 

used to estimate their inputs to the Yolo Bypass because they have similar land uses as the 

Ulatis Creek watershed. This assumption, and the resulting tributary load allocations, may need 

Delta Methylmercury TMDL Report 177 April 2010 

 
to be re-evaluated during the control program review. In addition, no methylmercury load 

estimates were made for other small drainage areas for which no methylmercury concentration 

data were available: Manteca-Escalon, Bethany Reservoir, Antioch, and Montezuma Hills 

areas). These areas contribute only about one third of a percent of all water inputs to the 

Delta/Yolo Bypass. Their methylmercury inputs to the Delta and Yolo Bypass are encompassed 

by the margin of safety incorporated in all other allocations (see Section 8.3 for more 

information about the margin of safety). Their potential methylmercury loading will be 

evaluated during the control program review and allocations assigned as needed. 

8.1.3 Calculation Methods for NPDES Facility Waste Load Allocations 

Staff assumed that, in general, NPDES-permitted WWTP discharges throughout the Delta/Yolo 

Bypass would increase by 120%. Staff assumed that half of that growth will be addressed by 

expansions to existing facilities in each Delta subarea, and that the remaining half will be 

serviced by new facilities in each subarea. Table 8.3 at the end of this section illustrates WWTP 

effluent volumes discharged to each Delta subarea (based on volumes identified in Table 6.5 in 

Chapter 6 for WWTPs that were discharging to surface water during the WY2000-2003 TMDL 

period), the amount of discharge volume increase expected in each subarea, and the discharge 

volume that staff assumed will be addressed by existing and new facilities. 

Results from methylmercury monitoring by NPDES facilities in the Delta and upstream tributary 

watersheds indicate that many facilities have average effluent methylmercury levels that 

approach or are less than the proposed implementation goal for unfiltered methylmercury in 

Delta waters (0.06 ng/l), while other facilities have much higher methylmercury levels (see 

Chapter 6 and Appendix G in the TMDL Report and Bosworth et al., 2010). This indicates that 

some discharges, though they contribute methylmercury loading to the Delta, may act as 

dilution because of their low methylmercury concentrations. 

Staff recommends that source discharges with average methylmercury concentrations below 

the proposed aqueous methylmercury goal of 0.06 ng/l be considered dilution and assigned a 

waste load allocation based on their existing discharge methylmercury concentration. There are 

four NPDES-permitted facilities that discharged during the WY2000-2003 TMDL period with 

effluent that had methylmercury concentrations less than 0.06 ng/l that still (as of February 

2010) discharge to surface water: Brentwood WWTP, Deuel Vocational Institute WWTP, 

Oakwood Lake Subdivision Mining Reclamation, and Woodland WWTP. The “Concentration 

Used to Calculate Allocation” in Table 8.4 for these sources was set at the existing discharge 

methylmercury concentration for each of these dischargers. 

Conceptually, there is no need to limit the loading from sources that act as dilution, given the 

overall extent of impairment throughout the Delta. However, to enable the calculation of 

allocations required for other sources, load-based allocations must be calculated even for those 

sources that act as dilution. Staff assumed that the three municipal WWTPs with discharges 

less than 0.06 ng/l would increase their discharge volume by 60% to account for future 

population growth, with one exception. The Central Valley Water Board recently adopted new 

waste discharge requirements for the City of Woodland WWTP (Order No. R5-2009-0010) that 

allow it to increase its design daily average effluent flow capacity from 7.8 mgd to 10.4 mgd. As 

a result, staff used 10.4 mgd rather than 160% of the WY2005 effluent flow (1.6 * 6.05 mgd = 

Delta Methylmercury TMDL Report 178 April 2010 

 
9.7 mgd). Staff calculated the methylmercury waste load allocations for the Brentwood WWTP 

and Deuel Vocational Institute WWTP shown in Table 8.4 by multiplying their existing average 

effluent methylmercury concentrations by their current discharge volumes (shown in Table 8.3) 

multiplied by 160%. 

Staff also calculated “Unassigned NPDES Facility Allocations” in Table 8.4 for each subarea to 

address new NPDES discharges. Staff assumed that new WWTPs would be designed to 

discharge effluent with methylmercury concentrations equal to or less than 0.06 ng/l, and 

calculated the “Unassigned WWTP allocations” by multiplying the predicted volumes shown in 

Table 8.3a by 0.06 ng/l methylmercury. As discussed in the footnotes for Table 8.3a, the 

predicted volumes have been modified since the February 2008 draft report to account for new 

facility discharges to surface water that recently began or are about to begin and therefore were 

given facility-specific allocations in Table 8.4. 

To calculate allocations for WWTPs with effluent methylmercury concentrations greater than 

0.06 ng/l, staff used the existing effluent volumes (rather than multiply the existing volumes by 

160%) and the percent allocation calculation method described in the next section. Although 

these facilities may need to increase their discharged effluent volumes in response to 

population growth in their service areas, increased effluent volumes at their existing effluent 

concentrations, if allowed, would worsen the methylmercury impairment. Conceptually, the 

discharge volume from a WWTP that has an average effluent methylmercury concentration 

greater than 0.06 ng/L could be allowed to increase so long as its methylmercury load does not 

increase. 45 This approach is consistent with State Water Board Resolution No. 2005-0060,46

which required the San Francisco Bay Water Board to incorporate provisions that acknowledge 

the efforts of those point sources whose effluent quality demonstrates good performance, and 

require improvement by other dischargers, when establishing waste load allocations. 

Several municipal WWTPs in the Delta/Yolo Bypass have ceased discharging to surface waters, 

others have begun discharging, one is expected to begin discharging in the near future, and two 

have had substantial changes in their effluent methylmercury levels since WY2003. In 

summary: 

• The San Joaquin County Service Area 31 Flag City WWTP, Walnut Grove WWTP, West 

Sacramento WWTP, and Rio Vista Trilogy WWTP have ceased discharging to surface 

water; 

• The Mountain House WWTP and Northwest WWTP began discharging to surface water; 

• The Ironhouse Sanitary District WWTP is expected to begin discharging to the San 

Joaquin River within the West Delta subarea within the next year; and 

 

45 Discharge volume from a WWTP that has average effluent methylmercury concentrations greater than 0.06 ng/l 

could be allowed to increase so long as its load does not increase above its wasteload allocation. For example, an 

increase in volume would necessitate a decrease in methylmercury concentration to maintain the load allocation so 

that the increased volume does not cause an increase in receiving water methylmercury concentration. Under 

circumstances described in the following pages, WWTPs that expand their discharge may also be allotted a portion 

of the “Unassigned NPDES Facility Allocations”. If an offset program is developed, another option could be for 

such a WWTP to compensate for increases in its load by completing offset projects upstream. 46 On September 7, 2005, the State Water Board adopted Resolution No. 2005-0060 (“Remand Order”) remanding 

the San Francisco Bay Water Board’s San Francisco Bay Mercury TMDL Amendment with requirements for 

specific revisions to the TMDL and associated implementation plan. 

Delta Methylmercury TMDL Report 179 April 2010 

 
• The Stockton WWTP and SRCSD Sacramento River WWTP have had substantial 

reductions in their effluent methylmercury concentrations and loads in recent years. 

Because the West Sacramento and Walnut Grove WWTPs discharged to surface waters during 

the TMDL period, WY2000-2003, their effluent methylmercury loads shown in Table 6.5 are 

included in the Table 6.2 load summary in Chapter 6. However, as part of regionalization 

efforts, SRCSD’s Sacramento River WWTP now receives influent that had been treated by the 

West Sacramento and Walnut Grove WWTPs. To address this change, the “Existing Average 

Annual MeHg Load” in Table 8.4 for the SRCSD Sacramento River WWTP reflects the sum of 

the effluent methylmercury loads presented in Table 6.5 for the SRCSD Sacramento River, 

West Sacramento and Walnut Grove WWTPs (160, 0.39, and 0.24 g/yr, respectively, for a sum 

of 160.63, rounded to 161 g/yr for allocation calculations); this sum was then multiplied by the 

“Percent Allocation” to calculate the waste load allocation for the SRCSD Sacramento River 

WWTP. The 2008-2009 Stakeholder Process’s NPDES Facility Workgroup evaluated several 

methods to calculate allocations that would fairly and equitably address regionalization efforts 

and selected this as the preferred method. 

The San Joaquin County Service Area 31 Flag City WWTP was discharging to surface water 

during the WY2000-2003 period. As a result, its effluent methylmercury load is included in the 

Table 6.2 summary in Chapter 6. However, the discharger recently completed the construction 

of a pump station and dual forcemain project that allows for discharge of the Flag City 

wastewater to the City of Lodi White Slough WWTP. As of 10 April 2008, all wastewater flows 

from the Flag City area are being directed to the Lodi WWTP, and the Flag City WWTP’s 

discharge to surface waters has ceased. To address this change, the “Existing Average Annual 

MeHg Load” in Table 8.4 for the Lodi and Flag City WWTPs were summed (0.93 and 

0.0066 g/yr, for a sum of 0.94 g/yr) and then multiplied by the “Percent Allocation” to calculate 

the waste load allocation for the Lodi WWTP. This is the same method used to address the 

regionalization of the SRCSD and West Sacramento WWTPs. 

If other NPDES facilities that have allocations in Table 8.4 regionalize or otherwise consolidate 

after the adoption of this TMDL, their waste load allocations can be summed. 

In 2007 the Trilogy WWTP was closed and the Northwest WWTP began to discharge in its 

place. Central Valley Water Board Order No. R5-2004-0092 considers the closure of the Trilogy 

WWTP coinciding with the start-up of the Northwest WWTP as a change in treatment process 

and location rather than as a new treatment plant. To address this change, the “Existing 

Average Annual MeHg Load” in Table 8.4 reflects the annual methylmercury load discharged by 

the Trilogy WWTP, which discharged 0.1 mgd. The Northwest WWTP has not yet completed 

effluent methylmercury monitoring; however, it has treatment processes in place that have 

resulted in very low effluent methylmercury concentrations at other WWTPs (see Section 6.2.3.1 

in Chapter 6 for more discussion about Northwest WWTP treatment processes and effluent 

methylmercury concentrations observed at WWTPs with similar treatment processes). As a 

result, the allocation for the Northwest WWTP in Table 8.4 is based on its current start-up 

capacity of 1 mgd, which is 10 times greater than the Trilogy WWTP discharge, and the current 

calibration standard for methylmercury analysis (0.05 ng/l), which results in a load of 0.069 g/yr. 

Because it is likely that the estimated effluent load for the Northwest WWTP may be an 

overestimate, given the very low effluent methylmercury concentrations observed at WWTPs 

Delta Methylmercury TMDL Report 180 April 2010 

 
that employ similar treatment processes, its allocation may include a margin of safety. As 

described in the draft Basin Plan Amendment staff report, staff recommends that a control 

program review take place after additional Delta-specific studies are completed, during which 

the Northwest WWTP allocation can be adjusted if needed. 

The Mountain House CSD WWTP was not discharging to surface water prior to March 2007 and 

therefore was not identified in the source analysis for the TMDL period, WY2000-2003. The 

Mountain House CSD WWTP now discharges to Old River within the San Joaquin River 

subarea. Because it is now discharging to surface water and has submitted effluent 

methylmercury concentration data for its discharge (see Section 6.2.3.1 and Appendix L), staff 

calculated a waste load allocation for its discharge. Between August 2007 and May 2009, 

21 monthly effluent samples were analyzed for methylmercury. Four results were reported as 

equal to the detection limit (0.05 ng/l) and 17 results were reported as “ND” (nondetect) with a 

method detection limit of 0.05 ng/l. The allocation was calculated using a methylmercury 

concentration of 0.05 ng/l and the facility’s average dry weather design flow of 5.4 mgd to obtain 

a waste load allocation of 0.37 g/year. 

The Ironhouse Sanitary District submitted a Report of Waste Discharge in June 2007 and in 

April 2008 received a NPDES permit (NPDES No. CA0085260) to discharge up to 4.3 mgd of 

treated wastewater from the Ironhouse Sanitary District (ISD) WWTP to the San Joaquin River 

off of Jersey Island in the West Delta subarea. As of February 2010, the ISD had not yet 

submitted a request for surface water discharge; however, it is expected to begin discharging 

within the next year. In the February 2008 draft TMDL report, the “unassigned allocation” for the 

West Delta subarea was based on the expected design flow for the ISD WWTP. Because the 

ISD WWTP has since received a NPDES permit to discharge, Table 8.4 now includes a waste 

load allocation specific to the ISD WWTP. The ISD has designed its new WWTP to include: 

coarse screening, grit removal, fine screening, anoxic basins, aeration basins, membrane 

filtration and UV disinfection. The effluent will be nitrified and denitrified and meet California 

Code of Regulations Title 22 disinfection requirements for both the surface water discharge and 

land disposal. Table 23 in “A Review of Methylmercury and Inorganic Mercury Discharges from 

NPDES Facilities in California’s Central Valley” (Bosworth et al., 2010) indicated that WWTPs 

that employed nitrification/denitrification, filtration and UV disinfection had effluent 

methylmercury concentrations that ranged from nondetect to 0.078 ng/l and average and 

median effluent methylmercury concentrations of 0.029 and 0.020 ng/l, respectively, based on 

three facilities and 21 samples, 11 of which had methylmercury concentrations less than the 

method detection limit. In the absence of monitoring data, it may not be reasonable to calculate 

a waste load allocation for the ISD WWTP based on a concentration that is less that the current 

calibration standard for methylmercury analysis (0.05 ng/l). As a result, its waste load was 

estimated using a concentration of 0.05 ng/l and discharge volume of 4.3 mgd to obtain an 

annual load of 0.030 g/year. 

Any new NPDES-permitted facilities that begin to discharge after this TMDL is adopted but are 

not identified in Table 8.4 would be allotted a portion of the “unassigned allocation” for the 

subarea where their discharges are located, so long as the sum of the new facilities’ discharge 

methylmercury loads does not exceed the unassigned allocations. “New” facilities could include 

newly built facilities that have not previously discharged to land or water as well as existing 

facilities that previously discharged to land and then began to discharge to surface water or 

Delta Methylmercury TMDL Report 181 April 2010 

 
diverted discharges to another facility that discharges to surface water as part of ongoing 

regionalization efforts. In addition, staff recommends that existing facilities also be allotted a 

portion of the unassigned allocations in the subareas where they discharge if they expand 

beyond their allocations listed in Table 8.4 so long as the additional allocation does not exceed 

the product of the net increase in flow volume and 0.06 ng/l methylmercury. The 2008-2009 

Stakeholder Process’s NPDES Facility Workgroup evaluated several approaches for allowing 

access to the “unassigned allocations” that would fairly and equitably address regionalization 

efforts and new discharges from existing and newly-built facilities and selected this as the 

preferred approach. The sum of all new and/or expanded methylmercury discharges from 

NPDES facilities within each Delta subarea must not exceed the Delta subarea-specific waste 

load allocation listed in Table 8.4. 

Two WWTPs, the City of Stockton WWTP and the SRCSD Sacramento River WWTP, have had 

marked decreases in effluent methylmercury concentrations and loads in recent years. As 

discussed previously in Chapter 6 (Section 6.2.3.1), upgrades to the City of Stockton WWTP 

completed in September 2006 appear to have led to reductions in total mercury and 

methylmercury as well as ammonia. A comparison of WWTP effluent methylmercury data 

collected before (August 2004-July 2005) and after (January-July 2009) the treatment plant 

upgrade indicates that since the WWTP was upgraded, average methylmercury effluent 

concentrations decreased by 91%. SRCSD’s Sacramento River WWTP had effluent 

methylmercury data for 2001-2007 that illustrated a marked decrease in effluent methylmercury 

and total mercury concentrations with time. During the April 2008 Board hearing meeting for the 

Delta mercury control program, the SRCSD District Engineer testified that implementation of the 

Be Mercury Free Program to reduce inorganic mercury sources to SRCSD’s WWTP resulted in 

reductions in both inorganic mercury and methylmercury discharges from the WWTP. Although 

more recent effluent data for the Stockton WWTP and SRCSD WWTP discharges indicate a 

change in the nature of their discharges, the allocations in Table 8.4 were calculated using the 

earlier data (August 2004 to July 2005 for the City of Stockton; December 2000 to June 2003 for 

the SRCSD WWTP) because the earlier data are more representative of conditions during the 

TMDL period, WY2000-2003. In addition, this approach ensures that the dischargers are not 

unfairly penalized for making early improvements to their discharges. 

The City of Davis WWTP (CA0079049) has two discharge locations; wastewater is discharged 

from Discharge 001 to the Willow Slough Bypass upstream of the Yolo Bypass and from 

Discharge 002 to the Conaway Ranch Toe Drain in the Yolo Bypass. The methylmercury load 

allocation listed in Table 8.4 applies only to Discharge 002, which discharges seasonally from 

about February to June. Discharge 001 is encompassed by the Willow Slough watershed 

methylmercury allocation. Discharge 001 will be assigned an individual allocation when a 

control program is developed for the upstream watersheds. 

As noted in Section 6.2.3, two of the NPDES-permitted facilities in the Delta are power or 

heating/cooling facilities that use ambient water for cooling water, Mirant Delta LLC Contra 

Costa Power Plant and the State of California Heating/Cooling Plant. Methylmercury loads and 

concentrations in heating/cooling and power facility discharges vary with intake water 

conditions; the facilities do not appear to act as a source of methylmercury to the Delta. Staff 

recommends that such facilities have concentration-based allocations equal to 100% of their 

intake methylmercury concentrations, so that their discharge allocations equal the detected 

Delta Methylmercury TMDL Report 182 April 2010 

 
methylmercury concentration found in their intake water. Outflows from the Mirant Delta plant 

were not incorporated in the allocation calculations for other sources in Section 8.1.4 and are 

not listed in Table 8.4. A concentration-based allocation for the Mirant Delta plant is listed in 

Table B in the proposed Basin Plan amendments provided at the beginning of the draft Basin 

Plan Amendment staff report. The State of California Heating/Cooling Plant recently ceased 

discharging and as a result is not assigned an allocation in the proposed Basin Plan 

amendments. 

GWF Power Systems (CA0082309), in the West Delta subarea, acquires its intake water from 

sources other than ambient surface water and therefore was incorporated in the allocation 

calculations in Section 8.1.4. GWF effluent methylmercury concentrations are less than the 

analytical method detection limit (0.03 ng/l; see Table 6.5 in Chapter 6). As a result, staff 

recommends that its allocation be equal to an annual load of 0.0052 g/yr, calculated by using 

the methylmercury method detection limit (0.03 ng/l) and GWF’s design flow (0.125 mgd) to 

accommodate potential growth. 

Discharge methylmercury data were not available for the Lincoln Center Groundwater 

Treatment Facility in Stockton, which discharges treated groundwater to Fourteenmile Slough in 

the Central Delta subarea. Other groundwater treatment facility discharges monitored to date 

have average methylmercury concentrations below current method detection limits (< 0.03 ng/l; 

Bosworth et al., 2010). As a result, staff recommends that allocation for the Lincoln Center 

Facility be equal to an annual load of 0.018 g/yr, calculated by using the design flow (0.43 mgd) 

and the methylmercury method detection limit (0.03 ng/l). This allocation can be modified at the 

end of Phase 1, after facility-specific discharge methylmercury data is collected. 

Discharge volumes and methylmercury data were not available for the Metropolitan Stevedore 

Company (CA0084174), a marine bulk commodity terminal on leased land at the Port of 

Stockton in the Central Delta subarea. Staff recommends that a methylmercury waste load 

allocation specifically for non-storm water discharges from the Metropolitan Stevedore Company 

be established in its NPDES permit once it completes at least three sampling events for 

methylmercury in its discharges. Its discharge will be allotted a portion of the “unassigned 

allocation” for the Central Delta subarea. 

As described in Section 8.1.3, several NPDES-permitted facilities have waste load allocations 

based on 160% of their existing loads or on their permitted design flows, rather than on their 

existing discharges. On Table 8.4, their allocations are shown as having two components, their 

existing loads and their allowable increase (“allowable future growth”). This was done so that a 

summary table (Table 8.5) could be created that clearly identifies the sum of allowable 

discharge load increases in each subarea. These two components are summed for each 

facility-specific allocation for compliance purposes in Table B in the proposed Basin Plan 

amendments provided at the beginning of the draft Basin Plan Amendment staff report. The 

“allowable future growth” component of the Northwest WWTP allocation (0.065 g/yr) is based on 

the difference between the estimated load discharged by the Trilogy WWTP during the 

WY2000-2003 TMDL period (0.0041 g/yr) and the Northwest WWTP’s allocation calculated from 

its average dry weather flow start-up capacity of 1 mgd and 0.05 ng/l (0.069 g/yr). Because the 

Mountain House CSD WWTP and Ironhouse Sanitation District WWTP did not discharge to 

surface water during the WY2000-2003 TMDL period, they have only “allowable future growth” 

Delta Methylmercury TMDL Report 183 April 2010 

 
allocations in Table 8.4. The “unassigned allocations” in Table 8.4 are also listed as “allowable 

future growth”. 

Space intentionally left blank. 

Delta Methylmercury TMDL Report 184 April 2010 

 
Table 8.3a: Total Existing Municipal WWTP Effluent Volume Discharged to Each Delta Subarea, 

Predicted Increases Due to Population Growth, and Volumes and Methylmercury Loads 

Predicted to Be Discharged by New WWTPs. 

Subarea 

Existing 

Effluent 

Volume 

(mgd) (a)

Predicted 

Increase 

(mgd) (b)

Effluent Volume 

Predicted to 

Be Discharged 

by New WWTPs

(mgd) (c)

Effluent MeHg Load 

Predicted to 

Be Discharged 

by New WWTPs

(g/yr) (d)

Central Delta (f) 6.1 7.3 3.7 0.31 

Marsh Creek 3.1 3.7 1.9 0.16 

Sacramento River 170 204 102 8.5 

San Joaquin River 43 52 20.6 [26] (e) 1.7 

West Delta (f) 0 (g) 6.9 (g) 2.6 (g) 0.22 

Yolo Bypass 8.5 10.2 5.1 0.42 

(a) “Existing Effluent Volume” is the sum of effluent volumes discharged by municipal WWTPs in each Delta subarea that 

discharged during the TMDL period, WY2000-2003, except for the West Delta subarea. 

(b) Staff assumed that, in general, NPDES-permitted WWTP discharges throughout Delta/Yolo Bypass would increase by 120% in 

response to predicted population growth in the region. 

(c) Staff assumed that half of the predicted 120% population growth would be addressed by expansions to existing facilities in 

each Delta subarea, and that the remaining half would be serviced by new facilities in each subarea. Staff predicted discharge

volumes to be serviced by new WWTPs by multiplying the “Existing Effluent Volume” discharged to each subarea by 0.6. 

(d) “Effluent MeHg Load Predicted to Be Discharged by New WWTPs” was calculated by multiplying the predicted effluent 

volumes by 0.06 ng/l methylmercury. These loads are the basis for the “Unassigned NPDES Facility Allocations” in Table 8.4. 

(e) The Mountain House CSD WWTP recently began to discharge to surface water. To address this new discharger, staff 

included a facility-specific allocation for the Mountain House CSD WWTP in Table 8.4 and subtracted its design flow of 

5.4 mgd from the predicted volume for new WWTPs in the San Joaquin River subarea in this table. 

(f) As noted in the previous section, ambient methylmercury concentrations in the Central and West Delta subareas equal or 

approach the proposed aqueous methylmercury goal of 0.06 ng/l, resulting in the need for little-to-no reductions in 

methylmercury inputs to these subareas. As a result, staff recommended that methylmercury source inputs to these subareas 

have allocations set at 100%. The Central Delta subarea receives flows from the Sacramento, Yolo Bypass, Mokelumne, and 

San Joaquin subareas. The West Delta subarea receives flows from the Central Delta and Marsh Creek subareas. These 

subarea inflows are expected to decrease substantially (e.g., 40-80%) as upstream mercury management practices take place 

because methylmercury source load reductions ranging from 44 to 80% are required for the upstream subareas to achieve 

their assimilative capacities. These reductions will provide ample assimilative capacity for the Unassigned NPDES Facility 

Allocations based on the “Effluent MeHg Load Predicted to Be Discharged by New WWTPs”. 

(g) There are no WWTPs currently discharging in the West Delta subarea. However, the Ironhouse Sanitary District submitted a 

Report of Waste Discharge in 2007 and in April 2008 received a NPDES permit to discharge up to 4.3 mgd of treated 

wastewater from the Ironhouse Sanitary District (ISD) WWTP to the San Joaquin River within the West Delta subarea. The 

ISD WWTP will likely begin discharging to the San Joaquin River sometime in 2010 and was given its own waste load 

allocation in Table 8.4. The ISD WWTP waste load allocation was calculated using its design flow rather than its expected 

initial discharge flow and therefore its allocation will address expected population growth for its service area. Staff calculated 

the “Predicted Increase” for the West Delta subarea by multiplying 4.3 mgd by 60% (rather than 120%) and adding the result 

(2.6 mgd) to 4.3 mgd, for a total of 6.9 mgd. Staff calculated the “Effluent Volume Predicted to Be Discharged by New 

WWTPs” using 2.6 mgd because the ISD WWTP allocation will accommodate expected population growth in its service area. 

Staff expects that the ISD WWTP allocation and “unassigned allocation” based on 2.6 mgd will provide adequate 

accommodation for future population growth. This is because a nearby wastewater district (the Delta Diablo Sanitation District

(DDSD), which discharges with the jurisdiction of the San Francisco Bay Water Board) has expressed interest in importing 

treated water from the Ironhouse Sanitary District for recycling (Darling, 2008). As described in the draft Basin Plan 

Amendment staff report, staff recommends that a Delta mercury control program review take place in about 7 years, during 

which the methods for calculating the unassigned allocations can be revised if needed. 

Delta Methylmercury TMDL Report 185 April 2010 

 
Table 8.3b: Predicted Effluent Volumes Used to Calculate Corresponding Methylmercury Loads for 

Municipal WWTPs that Discharge Effluent with Average Methylmercury Concentrations 

Less than 0.06 ng/l. 

Permittee (a)

NPDES 

Permit No. 

Existing Effluent 

Volume (mgd)

Predicted Effluent Volume 

Used To Calculate MeHg Loads 

for Allocations in 

Table 8.4 (a) (mgd)

Brentwood WWTP CA0082660 3.1 5.0 

Deuel Vocational Inst. WWTP CA0078093 0.47 0.75 

Woodland WWTP CA0077950 6.05 10.4 

(a) Staff assumed that, in general, NPDES-permitted WWTP discharges throughout Delta/Yolo Bypass would increase by 120% in 

response to predicted population growth in the region. Staff assumed that half of the population growth would be addressed 

by expansions to existing facilities in each Delta subarea, and that the remaining half would be serviced by new facilities in 

each subarea. Discharges from WWTPs with effluent methylmercury concentrations less than 0.06 ng/l act as dilution. Staff 

recommends that these facilities be assigned allocations calculated using their existing effluent methylmercury concentrations. 

To determine loads for use in Table 8.4, discharge volumes for these WWTPs were multiplied by 160% to allow for volume 

and load increases due to predicted population growth, with one exception. The Central Valley Water Board recently adopted 

new waste discharge requirements for the City of Woodland WWTP that allow it to increase its design daily average effluent 

flow capacity from 7.8 mgd to 10.4 mgd. As a result, staff used 10.4 mgd rather than 160% of the WY2005 effluent flow (1.6 * 

6.05 mgd = 9.7 mgd). 

8.1.4 Percent Allocation Calculations 

As described in Section 8.1.2, the following sources have allocations set equal to 100% of their 

existing methylmercury loads: atmospheric deposition and discharges from urban areas outside 

of MS4 service areas in all Delta subareas; and all point and nonpoint sources in the Central 

and West Delta subareas. Also, as described in Section 8.1.3, several NPDES-permitted 

facilities have waste load allocations based on 160% of their existing loads or on their permitted 

design flows, rather than on their existing discharges. 

Allocations for point and nonpoint sources that have their allocations set equal to 100% of their 

existing effluent methylmercury loads and point sources (NPDES facilities) that are allowed to 

increase their discharges because they act as dilution are referred to as “Pre-determined 

Allocations”. The following equation was used to determine the percent allocations and 

corresponding allocation loads for all other point and nonpoint sources needed to achieve the 

assimilative capacity in each Delta subarea identified in Table 8.2: 

Equation 8.3: (using the San Joaquin subarea as an example) 

Percent Allocation = 

 = Assimilative Capacity – Sum of Pre-determined Allocations 

 All existing loads – Sum (Existing loads for sources with Pre-determined Allocations) 

 = 195 g/yr – (2.7 g/yr + 0.0022 g/yr + 0.021 g/yr + 0.38 g/yr + 0.37 + 1.7 g/yr)

 528 g/yr – (2.7 g/yr + 0.0022 g/yr + 0.013 g/yr + 0.38 g/yr) 

= 36.2% 

 Ë Explanation: As shown in Table 8.4e, allocated methylmercury loads for atmospheric deposition and 

nonpoint urban runoff were set at existing levels (2.7 g/yr and 0.0022 g/yr, respectively). Deuel 

Vocational Institute WWTP and Oakwood Lake Subdivision Mining Reclamation have average 

Delta Methylmercury TMDL Report 186 April 2010 

 
discharge methylmercury concentrations less than 0.06 ng/l, and existing annual loads of 0.013 g/yr 

and 0.38 g/yr, respectively. Both are assigned allocations based on their existing methylmercury 

concentrations. The Deuel Vocational Institute WWTP’s corresponding allocation load of 0.021 g/yr 

incorporates a percent allocation of 160%. An allocation load of 0.37 g/yr was reserved for the 

Mountain House CSD WWTP, which began discharging effluent to surface water after the WY2000-

2003 TMDL period; the Mountain House CSD WWTP has effluent with low methylmercury 

concentrations (≤ 0.05 ng/l). In addition, an allocation load of 2.2 g/yr was reserved for new NPDESpermitted discharges expected to service population growth in the San Joaquin subarea (“unassigned 

NPDES Facility allocation”, see Table 8.3). 

The percent allocations were applied to every point source discharge methylmercury 

concentration and load – except those with Pre-determined Allocations – within each subarea to 

calculate corresponding waste load allocations using Equations 8.4 and 8.5. Methylmercury 

inputs from agricultural lands, wetlands, and open-water habitat are based on methylmercury 

loads produced in situ and therefore do not have corresponding concentrations. As a result, the 

percent allocations were applied to such nonpoint source loads within each subarea to calculate 

corresponding load allocations using only Equation 8.5. 

Equation 8.4: 

(using City of Stockton WWTP in the San Joaquin subarea as an example) 

MeHg Concentration Used to Calculate Allocation (ng/l) = 

= % Allocation * Existing average annual effluent MeHg conc. 

= 36.2% * 0.94 ng/l 

= 0.34 ng/l

Equation 8.5: 

MeHg Waste Load Allocation (g/yr) = 

= % Allocation * Existing average annual effluent MeHg load 

= 36.2% * 36 g/yr 

= 13 g/yr 

Sometimes Equation 8.4 resulted in an average methylmercury concentration less than 

0.06 ng/l, the proposed implementation goal for ambient water. The preferred allocation 

strategy described in the draft Basin Plan Amendment staff report entails that no discharger 

(e.g., WWTPs and MS4s) be required to reduce its discharge average methylmercury 

concentration to less than 0.06 ng/l. If Equation 8.4 resulted in a value less than 0.06 ng/l for a 

particular point source discharge, the “Concentration Used to Calculate Allocation” was set at 

0.06 ng/l and the allocation percent and equivalent load were calculated using the following 

equations: 

Equation 8.6a: (using the City of Tracy WWTP in the San Joaquin subarea as an example) 

 % Allocation = Proposed ambient water implementation goal

Existing average annual effluent MeHg Conc. 

 = 0.06 ng/l ÷ 0.14 ng/l 

 = 43% 

Delta Methylmercury TMDL Report 187 April 2010 

 
Equation 8.6b: 

 MeHg Allocation Load (g/yr) = % Allocation * Existing Annual MeHg Load 

 = 43% * 1.8 g/yr 

 = 0.77 g/yr 

Allocations for sources calculated using Equations 8.6a and 8.6b were then treated as “Predetermined Allocations” and included in Equation 8.3 to re-calculate the percent allocation. The 

ultimate purpose of this iterative set of calculations is to ensure that the sum of all 

methylmercury inputs to each Delta subarea does not exceed the assimilative capacity so that 

the proposed implementation goal for ambient water and proposed fish tissue mercury targets 

can be achieved in each subarea. Percent allocations often were calculated to one or more 

decimal places in order to equitably address a broad range of source loads in a manner that 

enabled the allocations to be summed without introducing substantial rounding errors. 

Table 8.4 is split into separate sections for each Delta subarea. The loads in the “MeHg Load/ 

Waste Load Allocation (g/yr)” column sum to the assimilative capacity for each subarea. 

Several loads in this column have more than two significant figures in order to avoid rounding 

errors when comparing the sum of the loads to the assimilative capacity. For compliance 

assessment purposes, staff recommends that all loads be rounded to two significant figures. In 

addition, for NPDES facilities that have two components to their allocations (existing and 

allowable future growth), the two components should be summed for compliance purposes. 

The methylmercury concentrations listed in the “MeHg Conc. Used to Calculate Allocation (ng/l)” 

column should not be used as effluent limits and should not be used to assess compliance with 

the load-based allocations. 

Table 8.5 provides a summary of the sums of existing source loads and allocations for each 

subarea. 

Space intentionally left blank. 

Delta Methylmercury TMDL Report 188 April 2010 

 
Table 8.4a: Allocations for Methylmercury Sources to the Central Delta Subarea

MeHg 

Source

Tributary 

or 

Permittee Permit #

Existing 

Average 

Annual 

MeHg Conc.

(ng/l) 

Existing 

Average 

Annual 

MeHg Load 

(g/yr) 

Percent 

Allocation

MeHg Conc. 

Used to 

Calculate 

Allocation 

(ng/l) 

MeHg Load/ 

Waste Load 

Allocation

(g/yr) 

LOAD ALLOCATIONS 

Agricultural Drainage NA (a) 37 100% NA 37 

Atmospheric Deposition NA 7.3 100% NA 7.3 

Open Water Habitats NA 370 100% NA 370 

Wetland Habitats NA 210 100% NA 210 

Tributary Bear/Mosher Creeks 0.31 11 100% 0.31 11 

Inputs Calaveras River 0.14 26 100% 0.14 26 

Urban runoff (nonpoint source) 0.24 0.14 100% 0.24 0.14 

WASTE LOAD ALLOCATIONS 

Discovery Bay WWTP CA0078590 0.18 0.37 100% 0.18 0.37 

Lincoln Center Groundwater 

Treatment Facility CA0084255 0.030 0.010 100% 0.030 0.010 

Lincoln Center Groundwater 

Treatment Facility 

(allowable future growth) 

CA0084255 NA NA 100% 0.030 0.0080 

Lodi White Slough WWTP CA0079243 0.15 0.94 100% 0.15 0.94 

Metropolitan Stevedore (b) CA0084174 To be determined. (b)

NPDES 

Facilities 

Unassigned NPDES Facility Allocation 

(allowable future growth) NA NA 100% 0.06 0.31 

Contra Costa (County of) CAS083313 0.24 0.75 100% 0.24 0.75 

Lodi (City of) CAS000004 0.24 0.053 100% 0.24 0.053 

Port of Stockton MS4 CAS084077 0.24 0.39 100% 0.24 0.39 

San Joaquin (County of) CAS000004 0.24 0.57 100% 0.24 0.57 

NPDES 

MS4s 

Stockton Area MS4 CAS083470 0.24 3.6 100% 0.24 3.6 

CENTRAL DELTA SUBAREA TOTAL: 0.060 668 100% 0.060 668 

(a) NA: not applicable. 

(b) No methylmercury or discharge volume data are available for Metropolitan Stevedore (CA0084174), a marine bulk commodity 

terminal in the Central Delta subarea. Staff recommends that a methylmercury waste load allocation specifically for non-storm 

water discharges from the Metropolitan Stevedore Company be established in its NPDES permit once it completes at least three 

sampling events for methylmercury in its discharges. Its discharge will be allotted a portion of the “unassigned allocation” for the 

Central Delta subarea. 

Delta Methylmercury TMDL Report 189 April 2010 

 
Table 8.4b: Allocations for Methylmercury Sources to the Marsh Creek Subarea

MeHg 

Source

Tributary 

or 

Permittee Permit #

Existing 

Average 

Annual 

MeHg Conc.

(ng/l) 

Existing 

Average 

Annual 

MeHg Load 

(g/yr) 

Percent 

Allocation

MeHg Conc. 

Used to 

Calculate 

Allocation 

(ng/l) 

MeHg Load/ 

Waste Load 

Allocation

(g/yr) 

LOAD ALLOCATIONS 

Agricultural Drainage NA (a) 2.2 18% NA 0.40 

Atmospheric Deposition NA 0.23 100% NA 0.23 

Open Water Habitats NA 0.18 18% NA 0.032 

Wetland Habitats NA 0.34 18% NA 0.061 

Tributary Inputs Marsh Creek 0.25 1.9 18% 0.045 0.34 

WASTE LOAD ALLOCATIONS 

Brentwood WWTP CA0082660 0.02 0.086 100% 0.02 0.086 

Brentwood WWTP 

(allowable future growth) NPDES CA0082660 NA NA 100% 0.02 0.054 

Facilities 

Unassigned NPDES Facility Allocation 

(allowable future growth) NA NA 100% 0.06 0.16 

NPDES MS4s Contra Costa (County of) CAS083313 0.24 1.2 25% 0.06 0.30 

MARSH CREEK SUBAREA TOTAL: 0.224 6.14 27% 0.060 1.66 

 (a) NA: not applicable. 

Table 8.4c: Allocations for Methylmercury Sources to the Mokelumne/Cosumnes Rivers Subarea

MeHg 

Source

Tributary 

or 

Permittee Permit #

Existing 

Average 

Annual 

MeHg Conc.

(ng/l) 

Existing 

Average 

Annual 

MeHg Load 

(g/yr) 

Percent 

Allocation

MeHg Conc. 

Used to 

Calculate 

Allocation 

(ng/l) 

MeHg Load/ 

Waste Load 

Allocation

(g/yr) 

LOAD ALLOCATIONS 

Agricultural Drainage NA (a) 1.6 35.7% NA 0.57 

Atmospheric Deposition NA 0.29 100% NA 0.29 

Open Water Habitats NA 4.0 35.7% NA 1.4 

Wetland Habitats NA 30 35.7% NA 11 

Tributary Inputs Mokelumne River 0.17 110 35.7% 0.086 39.3 

Urban (nonpoint source) 0.24 0.018 100% 0.24 0.018 

WASTE LOAD ALLOCATIONS 

NPDES MS4s San Joaquin (County of) CAS000004 0.24 0.045 35.7% 0.12 0.016 

MOKELUMNE/COSUMNES RIVERS SUBAREA TOTAL: 0.166 146 36% 0.060 52.6 

(a) NA: not applicable.

Delta Methylmercury TMDL Report 190 April 2010 

 
Table 8.4d: Allocations for Methylmercury Sources to the Sacramento River Subarea

MeHg 

Source

Tributary 

or 

Permittee Permit #

Existing 

Average 

Annual 

MeHg Conc.

(ng/l) 

Existing 

Average 

Annual 

MeHg Load 

(g/yr) 

Percent 

Allocation

MeHg Conc. 

Used to 

Calculate 

Allocation 

(ng/l) 

MeHg Load/ 

Waste Load 

Allocation

(g/yr) 

LOAD ALLOCATIONS 

Agricultural Drainage NA (a) 36 55.51% NA 20 

Atmospheric Deposition NA 5.6 100% NA 5.6 

Open Water Habitats NA 140 55.51% NA 78 

Wetland Habitats NA 94 55.51% NA 52 

Tributary Morrison Creek 0.10 7.5 55.51% 0.056 4.2 

Inputs Sacramento River 0.10 2,026 55.51% 0.056 1,125 

Urban (nonpoint source) 0.24 0.62 100% 0.24 0.62 

WASTE LOAD ALLOCATIONS 

Rio Vista WWTP CA0079588 0.16 0.10 55.51% 0.089 0.056 

Rio Vista Trilogy / 

Northwest WWTP CA0083771 0.06 0.0041 100% 0.06 0.0041 

Rio Vista Northwest WWTP 

(allowable future growth) CA0083771 NA NA 100% 0.05 0.065 

Sacramento Combined WWTP CA0079111 0.54 0.95 55.51% 0.30 0.53 

SRCSD Sacramento River WWTP CA0077682 0.72 161 55.51% 0.40 89 

NPDES 

Facilities 

Unassigned NPDES Facility Allocation 

(allowable future growth) NA NA 100% 0.06 8.5 

Rio Vista (City of) CAS000004 0.24 0.014 55.51% 0.13 0.0078 

Sacramento Area MS4 CAS082597 0.24 1.8 55.51% 0.13 1.0 

San Joaquin (County of) CAS000004 0.24 0.19 55.51% 0.13 0.11 

Solano (County of) CAS000004 0.24 0.073 55.51% 0.13 0.041 

West Sacramento (City of) CAS000004 0.24 0.65 55.51% 0.13 0.36 

NPDES 

MS4s 

Yolo (County of) CAS000004 0.24 0.073 55.51% 0.13 0.041 

SACRAMENTO RIVER SUBAREA TOTAL: 0.108 2,475 56% 0.060 1,385 

(a) NA: Not applicable. 

Delta Methylmercury TMDL Report 191 April 2010 

 
Table 8.4e: Allocations for Methylmercury Sources to the San Joaquin River Subarea

MeHg 

Source

Tributary 

or 

Permittee Permit #

Existing 

Average 

Annual 

MeHg Conc.

(ng/l) 

Existing 

Average 

Annual 

MeHg Load 

(g/yr) 

Percent 

Allocation

MeHg Conc. 

Used to 

Calculate 

Allocation 

(ng/l) 

MeHg Load/ 

Waste Load 

Allocation

(g/yr) 

LOAD ALLOCATIONS 

Agricultural Drainage NA (a) 23 36.1% NA 8.3 

Atmospheric Deposition NA 2.7 100% NA 2.7 

Open Water Habitats NA 48 36.1% NA 17 

Wetland Habitats NA 43 36.1% NA 16 

Tributary French Camp Slough 0.14 11 36.1% 0.051 4.0 

Inputs San Joaquin River 0.16 356 36.1% 0.058 129 

Urban (nonpoint source) 0.24 0.0022 100% 0.24 0.0022 

WASTE LOAD ALLOCATIONS 

Deuel Vocational Institute WWTP CA0078093 0.02 0.013 100% 0.02 0.013 

Deuel Vocational Institute WWTP 

(allowable future growth) CA0078093 NA NA 100% 0.02 0.008 

Manteca WWTP CA0081558 0.22 1.4 27% 0.06 0.38 

Mountain House CSD WWTP CA0084271 NA NA 100% 0.05 0.37 

Oakwood Lake Subdivision 

Mining Reclamation CA0082783 0.03 0.38 100% 0.03 0.38 

Stockton WWTP CA0079138 0.94 36 36.1% 0.34 13 

Tracy WWTP CA0079154 0.14 1.8 43% 0.06 0.77 

NPDES 

Facilities 

Unassigned NPDES Facility Allocation 

(allowable future growth) NA NA 100% 0.06 1.7 

Lathrop (City of) CAS000004 0.24 0.27 36.1% 0.087 0.097 

Port of Stockton MS4 CAS084077 0.24 0.010 36.1% 0.087 0.0036 

San Joaquin (County of) CAS000004 0.24 2.2 36.1% 0.087 0.79 

Stockton Area MS4 CAS083470 0.24 0.50 36.1% 0.087 0.18 

NPDES 

MS4s 

Tracy (City of) CAS000004 0.24 1.8 36.1% 0.087 0.65 

SAN JOAQUIN RIVER SUBAREA TOTAL: 0.160 528 37% 0.060 195 

(a) NA: Not applicable. 

Delta Methylmercury TMDL Report 192 April 2010 

 
Table 8.4f: Allocations for Methylmercury Sources to the West Delta Subarea

MeHg 

Source

Tributary 

or 

Permittee Permit #

Existing 

Average 

Annual 

MeHg Conc.

(ng/l) 

Existing 

Average 

Annual 

MeHg Load 

(g/yr) 

Percent 

Allocation

MeHg Conc. 

Used to 

Calculate 

Allocation

(ng/l) 

MeHg Load/ 

Waste Load 

Allocation

(g/yr) 

LOAD ALLOCATIONS 

Agricultural Drainage NA (a) 4.1 100% NA 4.1 

Atmospheric Deposition NA 2.4 100% NA 2.4 

Open Water Habitats NA 190 100% NA 190 

Wetland Habitats NA 130 100% NA 130 

Urban (nonpoint source) 0.24 0.066 100% 0.24 0.066 

WASTE LOAD ALLOCATIONS 

GWF Power Systems CA0082309 0.03 0.0019 100% 0.03 0.0019 

GWF Power Systems 

(allowable future growth) CA0082309 NA NA 100% 0.03 0.0033 

Ironhouse Sanitation District 

(allowable future growth) CA0085260 NA NA 100% 0.05 0.030 

Mirant Delta LLC Contra 

Costa Power Plant (b) CA0004863 Concentration-based allocation. (b)

NPDES Facilities 

Unassigned NPDES Facility Allocation 

(allowable future growth) NA NA 100% 0.06 0.22 

NPDES MS4s Contra Costa (County of) CAS083313 0.24 3.2 100% 0.24 3.2 

WEST DELTA SUBAREA TOTAL: 0.083 330 100% 0.060 330 

(a) NA: not applicable. 

(b) Methylmercury loads and concentrations in heating/cooling and power facility discharges vary with intake water conditions; the 

facilities do not appear to act as a source of methylmercury to the Delta. Staff recommends that Mirant Delta LLC Contra Costa

Power Plant a have concentration-based allocation equal to 100% of its intake methylmercury concentrations, so that its discharge 

allocation equals the detected methylmercury concentration found in its intake water. Outflows from the Mirant Delta plant were not 

incorporated in the allocation calculations for other sources. A concentration-based allocation for the Mirant Delta plant is listed in 

Table B in the proposed Basin Plan amendments provided at the beginning of the draft Basin Plan Amendment staff report. 

Delta Methylmercury TMDL Report 193 April 2010 

 
Delta Methylmercury TMDL Report 194 April 2010 

 

Table 8.4g: Allocations for Methylmercury Sources to the Yolo Bypass Subarea

MeHg 

Source

Tributary 

or 

Permittee Permit #

Existing 

Average 

Annual 

MeHg Conc.

(ng/l) 

Existing 

Average 

Annual 

MeHg Load 

(g/yr) 

Percent 

Allocation

MeHg Conc. 

Used to 

Calculate 

Allocation 

(ng/l) 

MeHg Load/ 

Waste Load 

Allocation

(g/yr) 

LOAD ALLOCATIONS 

Agricultural Drainage NA 19 21.5% NA 4.1 

Atmospheric Deposition NA 4.2 100% NA 4.2 

Open Water Habitats NA 100 21.5% NA 22 

Wetland Habitats NA 480 21.5% NA 103 

Cache Creek Settling 

Basin Outflow 0.50 140 21.5% 0.108 30 

Dixon Area 0.24 3.6 21.5% 0.052 0.77 

Fremont Weir 0.10 180 21.5% 0.022 39 

Knights Landing Ridge Cut 0.19 100 21.5% 0.041 22 

Putah Creek 0.18 11 21.5% 0.039 2.4 

Ulatis Creek 0.24 9.5 21.5% 0.052 2.1 

Tributary 

Inputs 

Willow Slough 0.24 18 21.5% 0.052 3.9 

WASTE LOAD ALLOCATIONS 

Davis WWTP (a) CA0079049 0.61 0.78 21.5% 0.13 0.17 

Woodland WWTP CA0077950 0.03 0.25 100% 0.03 0.25 

Woodland WWTP 

(allowable future growth) CA0077950 NA NA 100% 0.03 0. 18 

NPDES 

Facilities 

Unassigned NPDES Facility Allocation 

(allowable future growth) NA (b) NA 100% 0.06 0.42 

Solano (County of) CAS000004 0.24 0.085 25% 0.06 0.021 

West Sacramento (City of) CAS000004 0.24 1.1 25% 0.06 0.28 

NPDES 

MS4s 

Yolo (County of) CAS000004 0.24 0.33 25% 0.06 0.083 

YOLO BYPASS [North & South] SUBAREA TOTAL: 0.273 1,068 22% 0.060 235 

(a) The City of Davis WWTP (CA0079049) has two discharge locations; wastewater is discharged from Discharge 001 to the Willow 

Slough Bypass upstream of the Yolo Bypass and from Discharge 002 to the Conaway Ranch Toe Drain in the Yolo Bypass. The 

methylmercury load allocation listed in this table applies only to Discharge 002, which discharges seasonally from about 

February to June. Discharge 001 is encompassed by the Willow Slough watershed methylmercury allocation and will be 

assigned a facility-specific allocation when a control program is developed for the upstream watersheds. 

(b) NA: Not applicable. 
Table 8.5: Methylmercury Load and Waste load Allocations for Each Delta Subarea by Source Category

DELTA SUBAREA 

Central Delta Marsh Creek 

Mokelumne 

River 

Sacramento 

River 

San Joaquin 

River West D

 Source Type Current Load 

(g/yr) 

Allocation 

(g/yr) 

Current

Load

(g/yr) 

Allocation

(g/yr) 

Current

Load

(g/yr) 

Allocation

(g/yr) 

Current

Load 

(g/yr) 

Allocation 

(g/yr) 

Current

Load 

(g/yr) 

Allocation

(g/yr) 

Current

Load 

(g/yr) 

A

Methylmercury Load AllocationsAgricultural drainage (d) 37 37 2.2 0.40 1.6 0.57 36 20 23 8.3 4.1 Atmospheric wet deposition 7.3 7.3 0.23 0.23 0.29 0.29 5.6 5.6 2.7 2.7 2.4 Open water 370 370 0.18 0.032 4.0 1.4 140 78 48 17 190 Tributary Inputs (a) 37 37 1.9 0.34 110 39 2,034 1,129 367 133 Inputs from Upstream Subareas (b) (b) - - - - - - - - - - - - - - - - - - - - - - - - (b) Urban (nonpoint source) 0.14 0.14 --- --- 0.018 0.018 0.62 0.62 0.0022 0.0022 0.066 Wetlands (d) 210 210 0.34 0.061 30 11 94 52 43 16 130 Methylmercury Waste Load AllocationsNPDES facilities (a) 1.3 1.3 0.086 0.086 0 0 162 90 40 15 0.0019 NPDES facilities future growth (a) --- 0.32 (b) --- 0.21 --- 0 --- 8.6 --- 2.1 --- NPDES MS4 (a) 5.4 5.4 1.2 0.30 0.045 0.016 2.8 1.6 4.8 1.7 3.2 Total Loads (c) (g/yr) 668 668 6.14 1.66 146 52.6 2,475 1,385 528 195 330 (a) Values shown for Tributary Inputs, NPDES Facilities, NPDES Facilities Future Growth, and NPDES MS4 represent the sum of several individual dischar

allocations for the individual discharges that should be used for compliance purposes. 

(b) The Central Delta subarea receives flows from the Sacramento, Yolo Bypass, Mokelumne, and San Joaquin subareas. The West Delta subarea receive

and Marsh Creek subareas. These within-Delta flows have not yet been quantified because additional data are needed for loss rates across the subarea

inflows are expected to decrease substantially (e.g., 40-80%) as upstream mercury management practices take place. As a result, reductions for sourcesubareas and tributaries that drain directly to these subareas are not required. The Central Valley Water Board can consider modification of the allocatio

new allocations (e.g., for within-Delta flows between subareas) during the program review proposed to take place in about seven years based on existing 

becomes available. 

(c) The sum of all allocations for each subarea equals the assimilative load capacity for that subarea. Because calculations were completed prior to roundin

to totals. 

(d) The load allocations apply to the net methylmercury loads, where the net loads equal the methylmercury load in outflow minus the methylmercury loads 

water and precipitation). 

Delta Methylmercury TMDL Report 195 April 2010 
8.2 Total Mercury Load Reduction Requirement for Tributary Watersheds 

Methylmercury production is a positive linear function of the inorganic mercury content of 

sediment (see Chapter 3). Inorganic mercury load reductions elsewhere have resulted in 

decreases in fish tissue methylmercury concentrations (Table 3.1). It is expected that similar 

reductions in fish tissue concentration also will occur in the Delta once the mercury content of its 

sediment decreases. Staff recommends that inorganic (total) mercury requirements be 

implemented by the Delta mercury control program in addition to the methylmercury allocations 

for several reasons: (1) to maintain compliance with the USEPA’s criterion of 50 ng/l for total 

mercury in the water column; (2) to prevent increases in total mercury discharges resulting from 

population growth and other land use changes, which could cause increases in aqueous and 

fish methylmercury in the Delta, thereby worsening the impairment; (3) to comply with the San 

Francisco Bay TMDL allocation to the Central Valley; and (4) to help enable compliance with the 

open-water methylmercury load allocations described in the previous section. The TMDL for 

San Francisco Bay assigned the Central Valley a five-year average total mercury load allocation 

of 330 kg/yr or a decrease of 110 kg/yr (Section 2.4.2.3). 

As described in Chapter 4 of the draft Basin Plan Amendment staff report, the preferred TMDL 

implementation alternative entails: 

• NPDES Permitted Facilities in the Delta and Yolo Bypass: Implement pollutant 

minimization programs and maintain performance-based total mercury load limits during 

the first phase of Delta TMDL control program implementation. 

• NPDES Permitted (MS4) Urban Runoff Dischargers in the Delta and Yolo Bypass: 

Implement best management practices (BMPs) to control erosion and sediment 

discharges consistent with their existing permits and orders with the goal of reducing 

mercury discharges (all MS4s), and implement mercury-specific pollution prevention 

measures and BMPs to minimize inorganic mercury discharges (the largest three MS4s 

[Sacramento, Contra Costa and Stockton MS4s]). 

• Nonpoint Sources in the Delta and Yolo Bypass: Implement reasonable, feasible actions 

to reduce sediment in runoff with the goal of reducing inorganic mercury loading to the 

Yolo Bypass and Delta, in compliance with existing Basin Plan objectives and 

requirements, and Irrigated Lands Regulatory Program requirements. 

• Tributary Watershed Inputs to the Delta and Yolo Bypass: Total mercury load reduction of 

a minimum of 110 kg/yr. 

This section of the TMDL report reviews how the total mercury load reduction requirement 

maybe achieved in tributary watersheds. Total mercury reduction strategies for point and 

nonpoint sources in the Delta and Yolo Bypass are described in Chapter 4 of the draft Basin 

Plan Amendment staff report. 

The total mercury source analysis described in Chapter 7 indicates that almost all the total 

mercury loading (>97%) to the Delta and Yolo Bypass comes from tributary inputs. It could be 

argued that assigning total mercury load reduction requirements could wait until the upstream 

TMDLs are developed. Also, there is limited information available about total mercury loads 

contributed by individual sources in the tributary watersheds. However, there is abundant 

Delta Methylmercury TMDL Report 196 April 2010 

 
information about which watersheds contribute the most mercury-contaminated sediment. In 

addition, substantial mercury reductions – 110 kg/yr – are required for Central Valley inputs to 

the San Francisco Bay by the San Francisco Bay mercury control program. It is likely that total 

mercury reduction efforts in the watersheds, and subsequent methylmercury reductions in openwater, wetland and agricultural areas in the Delta, will take place more quickly if watershed total 

mercury load reduction requirements are included in the Delta mercury control program. 

A reduction of 110 kg/yr represents about a 28% decrease in the 20-year average annual 

loading47 from Delta tributaries (Table 7.1). Initial reduction efforts should focus on watersheds 

that export the largest volume of highly contaminated sediment, such as the Cache Creek, 

Feather River, American River, Cosumnes River, and Putah Creek watersheds (refer to 

Sections 7.1.1 and 7.4.1 and Tables 7.5 and 7.17 in Chapter 7). 

The Cache Creek Settling Basin (CCSB) is a 3,600-acre structure located at the base of the 

Cache Creek watershed. The U.S. Army Corp of Engineers initially constructed the CCSB in 

1937 to contain sediment and maintain the flood capacity of the Yolo Bypass. The CCSB was 

modified in 1993 to increase its sediment trapping efficiency. However, no provision was made 

for removing the additional trapped material. 

Most of the mercury in Cache Creek is transported on sediment. Therefore, an increase in 

sediment trapping also results in deposition and retention of mercury. The CCSB currently traps 

about half of the sediment and mercury transported by Cache Creek (Foe and Croyle, 1998; 

CDM, 2004; Cooke et al., 2004; CDM, 2004; Appendices F and I). The rest is exported to the 

Delta through the Yolo Bypass. 

Trapping efficiency calculations vary based on the period evaluated and the calculation method. 

For example, Board staff estimated that the basin receives about 224 kg/yr total mercury from 

the Cache Creek watershed and discharges about 118 kg/yr to the Yolo Bypass (a trapping 

efficiency of about 47%), based on annual load estimates for a 20-year period (WY1984-2003, a 

period with an even mix of wet and dry years) derived from statistically-significant correlations 

between water column total mercury concentrations and flows (refer to Chapter 7 and Appendix 

I for load calculation methods). CDM estimated that about 64% of the sediment and total 

mercury mass input to the basin is trapped when the volumes of sand, uncompacted silt and 

clay are converted to sediment mass over a modeled 35-year period (see CDM, 2004b, Table 4-

3). Although trapping efficiency calculations vary, they all indicate that substantial mercury 

loads are currently trapped in the basin. However, even though the basin traps a large portion 

of the mercury that comes into it, Cache Creek still accounts for about 60% of all inorganic 

mercury that enters the Yolo Bypass. 

The sediment/mercury trapping efficiency of the CCSB is expected to decrease as it fills and 

may reach zero in about 35 years unless a maintenance program is instituted to periodically 

remove material (CDM, 2004). A non-operational CCSB would result in a mercury discharge to 

the Yolo Bypass and Delta of about 224 kg/yr, an addition of 106 kg/yr mercury loading 

(Table 7.6b). 

 

47 Year-to-year loads are expected to fluctuate with rainfall and river flow conditions and other environmental factors. 

Delta Methylmercury TMDL Report 197 April 2010 

 
Two sets of actions are considered in the draft Basin Plan Amendment staff report (Chapter 4 

and Appendix C) for the Cache Creek Settling Basin that would reduce mercury discharges to 

the Yolo Bypass and Delta. First, mercury loads entering the CCSB from the Cache Creek 

watershed could be reduced. The Basin Plan Amendment for control of mercury in Cache 

Creek was adopted by the Central Valley Water Board in October 2005. Implementation actions 

described in the Basin Plan Amendment report would reduce mercury loads entering the Cache 

Creek Settling Basin by about 60 kg/year (Cooke and Morris, 2005), from a 20-year average of 

224 kg/yr to 164 kg/yr. Assuming a long-term basin trapping efficiency of about 47%, the 

watershed implementation actions would reduce basin total mercury mass discharges to the 

Yolo Bypass by about 31 kg/yr. Approximately 25 kg of the 60 kg/year reduction in the Cache 

Creek watershed may come from instituting control programs at all major mercury mines in the 

watershed.48 The remainder of the reduction will be achieved by control of erosion in mercuryenriched areas and by remediation/removal of contaminated floodplain sediment in the Cache 

Creek canyon and in Bear Creek. However, most the total mercury load now leaving the CCSB 

appears to originate from erosion of mercury contaminated sediment downstream of the mines. 

The Cache Creek mercury control program requires studies to evaluate in-stream sediment 

control options. It is unclear whether environmentally acceptable, cost effective control 

programs can be developed to significantly curtail the movement of this material. 

A second set of actions could focus on decreasing the mercury load leaving the Cache Creek 

Settling Basin. A program should be instituted to (a) periodically excavate the material presently 

accumulating in the CCSB, and (b) make additional modifications to the CCSB to increase 

trapping efficiency. Initial modeling results indicate that CCSB operation and design could be 

modified to improve the mercury mass trapping efficiency of the CCSB from to about 75% 

(CDM, 2004, Table 4-3, Alternative 5 - Excavate and Raise Weir Early). Decreasing mercury 

inputs to the CCSB from 224 to 164 kg/yr through the watershed control program and increasing 

the trapping efficiency of the CCSB from 47% to 75% results in an export to the Yolo Bypass of 

41 kg/yr, which represents a decrease of 77 kg/yr from current loading. This reduction is 

approximately 70% of the 110-kg/yr reduction required by the San Francisco Bay mercury 

TMDL. Based on these calculations, the February 2008 Basin Plan Amendment draft staff 

report included a numeric total mercury load limit of 41 kg/yr for outflow from the Cache Creek 

Settling Basin to the Yolo Bypass. 

However, after the release of the February 2008 draft report, DWR staff indicated that a more 

comprehensive feasibility study must take place to determine whether a 75% trapping efficiency 

is possible and to incorporate a stakeholder process so that local communities’ concerns about 

potential flood hazards resulting from modifying the basin can be addressed. The 2008-2009 

Stakeholder Process participants (including staff from the Central Valley Water Board, DWR 

and other agencies responsible for basin operations and other stakeholders) developed 

recommendations for Basin Plan amendment requirements that entail evaluating and 

implementing feasible total mercury load reductions for basin outflows up to and including a 

50% reduction from existing loads in place of a numeric load limit. A 50% reduction in existing 

loads (118 kg/yr) results in a total mercury load to the Yolo Bypass of about 59 kg/yr, compared 

to the 41 kg/yr described in the previous paragraph. 

 

48 The mines are located in Harley Gulch, Sulfur and Bear Creeks and Clear Lake. 

Delta Methylmercury TMDL Report 198 April 2010 

 
Table 8.6 provides a preliminary scoping of potential watershed total mercury load reductions 

(including the Cache Creek watershed) based on the assumption that it will be possible to 

reduce mercury loads from watersheds that discharge mercury-contaminated sediment (as 

indicated by relatively high TotHg:TSS ratios) by at least 50%. Staff used a 50% reduction rate 

because in watersheds with known, significant anthropogenic sources of mercury (primarily 

mining), the anthropogenic contribution is more than 50% of the total concentration of mercury 

in sediment. For example, the Feather River, American River, Cosumnes River have 

suspended sediment mercury concentrations that are more than twice the mercury 

concentration of suspended sediment in the Sacramento River upstream of Colusa, a 

watershed with a much lower density of mine sites (see Table 8.6 at the end of this section and 

Table 14 in Louie and others’ 2008 CalFed study). The sum of potential reductions based on 

this assumption is about 125 kg/yr. A 50% reduction in total mercury loads contributed by the 

four watersheds that discharge sediment that is most highly contaminated with mercury – 

Feather River, Cache Creek, American River and Putah Creek – alone would result in a 

104 kg/yr reduction. 

The suite of potential total mercury reduction actions identified by the “Regional Mercury Load 

Reduction Evaluation, Central Valley, California”, completed by Tetra Tech EM Inc. under 

contract to the USEPA (Tetra Tech, 2008), and the review of reasonably foreseeable methods 

of compliance in Chapter 4 of the draft Basin Plan Amendment staff report, indicates that the 

potential reductions outlined in Table 8.5 may be possible. However, additional feasibility 

analyses and stakeholder input are needed in order to evaluate alternatives, funding sources, 

and potential environmental concerns associated with potential projects. 

Given these factors, staff recommends that the Delta mercury control program include a 

110 kg/yr total mercury reduction requirement assigned jointly to the tributaries that drain to the 

Delta to ensure compliance with the San Francisco Bay mercury control program’s requirements 

for the Central Valley. Initial reduction efforts should focus on the four watersheds that 

discharge the most highly-contaminated sediment (Feather River, Cache Creek, American River 

and Putah Creek, all in the Sacramento Basin). Although it is not as large a source of total 

mercury loading, the Cosumnes River watershed in the San Joaquin Basin also would be an 

effective candidate for total mercury reduction projects because of its high mercury 

concentrations in suspended sediment. Several other watershed characteristics make the 

Cosumnes River an attractive candidate for remediation efforts during the initial implementation 

phases of the Delta and upstream mercury control programs: 

• As described in Section 7.1.1.2, not only does the Cosumnes River watershed have a 

history of hydraulic gold mining, it exports six times as much mercury to the Delta as the 

Mokelumne River watershed and is the largest river on the west-slope Sierra Nevada 

without a major dam, allowing unimpaired downstream movement of storm runoff. 

• The highest fish tissue levels observed in the Delta were in the lower Cosumnes River 

(Davis et al., 2008; Slotton et al., 2007). Extensive multi-year and seasonal fish mercury 

monitoring conducted in the lower Cosumnes River after the development of this TMDL 

source analysis observed small fish mercury levels that were 5 to 29 times the small fish 

mercury objective proposed in Chapter 3 of the draft Basin Plan Amendment report 

(Slotton et al., 2007). Slotton and others (2007, pages 58-59) observed extreme (400-

500%) increases in silverside mercury at the Cosumnes site in July 2006, when 

Delta Methylmercury TMDL Report 199 April 2010 

 
concentrations in 45-75 mm (2-3 inch) silversides reached levels averaging an 

“astounding” 0.869 ppm, with individual fish as high as 2.0 ppm. According to the authors, 

“these were concentrations that should be of serious concern, particularly in relation to 

wildlife exposure.” Slotton and others (2007) noted that their extensive seasonal 

sampling indicated that the very high 2006 silverside mercury concentrations in the lower 

Cosumnes River were traceable to an extreme, seasonal pulse event of highly elevated 

exposure linked to episodic flooding of the Cosumnes floodplain and observed that other 

small fish species with slower turnover rates than silversides (e.g., juvenile bass and 

prickly sculpin) exhibited much slower declines from peak mercury levels, with highly 

elevated concentrations persisting for many months. 

• Foe and others’ 2008 CalFed study found that water methylmercury concentrations in the 

Cosumnes River were the highest of any tributary to the Delta, consistent with the fish 

tissue data. The mean and 95% confidence limits for the Cosumnes and Mokelumne 

Rivers are 0.38±0.12 and 0.11±0.01 ng/l methylmercury, respectively (Foe et al., 2008, 

Table 2), compared to 0.17 ng/l methylmercury for the Mokelumne River downstream of 

its confluence with the Cosumnes River (Table 6.2 in Chapter 6). 

• As illustrated in Figure 6.3, the lower Cosumnes River has numerous wetland areas, and 

large wetland restoration efforts are planned for the lower Cosumnes River watershed 

within the Delta in the near future (e.g., Turner, 2009). 

Staff recommends that compliance with the proposed 110 kg/yr total mercury reduction 

requirement be assessed for the tributary inputs based on WY1984-2003 average annual loads. 

This 20-year period includes a mix of wet and dry years that is statistically similar to water years 

in the Sacramento Basin in the last 100 years. The proposed reduction will enable Delta waters 

to maintain compliance with the CTR criterion of 50 ng/l (Section 7.4 in Chapter 7). 

Additional total mercury and methylmercury reductions likely will be needed from most if not all 

of the watersheds to address the methylmercury impairment in each area of the Delta subareas 

and impairments specific to upstream watersheds. Specific limits for individual watershed 

exports should not be defined in the Delta mercury control program in order to allow for greater 

flexibility in developing upstream control strategies. Feasibility studies may show that particular 

projects could reduce mercury loads by more than 50% without causing other environmental 

impacts. However, the sum of the load reductions for the watershed exports needs to equal a 

minimum of 110 kg/yr. Most of the watersheds that drain to the Delta contain waterways 

already identified on the CWA Section 303(d) List as impaired by mercury. Hence, most will be 

the focus of future watershed-specific TMDL programs. Specific load reductions for each 

watershed will be assigned in control programs for the upstream watersheds. 

It is important to note that implementing only the inorganic mercury reductions described above 

will not adequately reduce methylmercury levels in the Delta in the near term (the proposed 

compliance date in the proposed Basin Plan amendments in the draft Basin Plan Amendment 

staff report is 2030). Because movement of contaminated sediment in the river channels is 

relatively slow, it is expected to take many years (e.g., a century or more) before the full benefit 

of inorganic mercury reductions in tributaries is seen in the Delta. (For additional discussion of 

the estimated time to reduce inorganic mercury inputs and attain fish tissue objectives, please 

refer to “Staff’s Initial Responses to Board and Stakeholder Questions and Comments at the 

Delta Methylmercury TMDL Report 200 April 2010 

 
April 2008 Hearing”, items 3 and 44, available on the Board website.) In addition, many of the 

tributary input methylmercury allocations developed in Section 8.1 entail methylmercury load 

reductions of 60% to 80%. Assuming that inorganic mercury loads could be reduced by 50% in 

these tributaries, reducing inorganic mercury alone would be insufficient to achieve the 

allocations. Staff expects that methylmercury management practices and very aggressive 

implementation of inorganic mercury reduction projects will be needed in the tributary 

watersheds, along with natural erosion, to achieve the tributary methylmercury load allocations. 

Table 8.5: Preliminary Evaluation of Potential Watershed Total Mercury Load Reductions 

Basin Watershed 

303(d) Listed

for Mercury 

Impairment 

Annual 

TotHg Load

(kg/yr)

TotHg:TSS 

(mg/kg)

Potential 

% Reduction & 

Corresponding 

Load Reduction (a) 

(kg/yr)

American River √ 14 0.27 50% 7 

Cache Creek Settling Basin √ 118 0.45 50% 59 

Colusa Basin Drain (Proposed) 13 0.09 5% 0.65 

Feather River √ 67 0.31 50% 34 

Morrison Creek 0.83 0.15 20% 0.17 

Natomas East Main Drain 3.0 0.38 – 0.64 50% 1.5 

Putah Creek √ 8.8 0.55 50% 4.4 

Sacramento River above 

Colusa 

√ 151 0.12 5% 7.6 

Sacramento Slough / Sutter 

Bypass 

√ 25 0.13 5% 1.3 

Sacramento (b)

Ulatis Creek 2.2 0.11 5% 0.11 

French Camp Slough 1.7 0.30 - 0.70 50% 0.85 

Marsh Creek √ 0.54 0.12 - 0.45 50% 0.27 

Cosumnes River 

upstream of I-5 48 0.41 50% 24 

Mokelumne River upstream of 

the Cosumnes River √ 8.4 0.22 50% 2.3 

San Joaquin (c)

San Joaquin River √ 29 0.13 5% 1.5 

(a) For scoping purposes only, a conservative 50% reduction was assumed to be likely needed for watershed total mercury loads in 

order to achieve tributary input allocations assigned by the Delta TMDL as well as to address upstream impairments. A lower 

percent reduction was assumed for watersheds that may discharge less mercury-contaminated material, as indicated by low 

TotHg:TSS ratios. Greater or lesser reductions may be determined to be necessary once upstream feasibility analyses have taken

place as part of upstream control programs. Total mercury loads were obtained from Tables 7.1 and 7.6b, and TotHg:TSS ratios 

were obtained from Table 7.17; values for the Cosumnes and Mokelumne Rivers were obtained from Louie and others’ 2008 

CalFed study. The annual TotHg loads represent the average annual loads estimated for WY1984-2003. This 20-year period 

includes a mix of wet and dry years that is statistically similar to what has occurred in the Sacramento Basin over the last 100 

years. Annual loads are expected to fluctuate with rainfall and river flow conditions and other environmental factors. 

(b) A total mercury load estimate is not available for Willow Slough, which drains to the Yolo Bypass in the Sacramento Basin. As a 

result, although it has a methylmercury allocation that requires substantial reductions, it is not included in this table. 

(c) The Calaveras River and Bear and Mosher Creeks in the San Joaquin Basin drain to the Central Delta subarea. Methylmercury 

allocations for these watersheds do not entail reductions; as a result, they are not included in this table. 

Delta Methylmercury TMDL Report 201 April 2010 

 
8.3 Margin of Safety 

Implicit and explicit margins of safety are included in the aqueous methylmercury goal for the 

Delta. In addition, while not a direct margin of safety, the implementation plan (Chapter 4 in the 

draft Basin Plan Amendment staff report) calls for updated fish advisories in the Delta and an 

expanded outreach program to educate humans fishing in the Delta. 

The proposed aqueous methylmercury goal of 0.06 ng/l (Chapter 5) incorporates an explicit 

margin of safety of approximately 10%. The linkage analysis (Section 5.2) predicted a safe 

level of 0.066 ng/l for average aqueous methylmercury, from which 0.006 was subtracted to 

provide a margin of safety. 

In addition, there is an implicit margin of safety for wildlife species that consume Delta fish. As 

outlined in the previous paragraph, the aqueous methylmercury goal corresponds to 0.24 mg/kg 

mercury in large TL4 fish, which was calculated for the protection of humans consuming about 

one meal per week. As shown in Table 4.9 (Chapter 4), the wildlife targets for smaller and 

lower trophic level fish correspond to large TL4 fish mercury levels that range from 0.30 mg/kg 

(for Western grebe) to 1.12 mg/kg (for Western snowy plover). These values correspond to 

350-mm largemouth bass mercury levels of 0.31 and 1.34 mg/kg. When entered into the 

regression equation for largemouth bass and unfiltered average aqueous methylmercury 

(Figure 5.2[A]), these values translate to aqueous methylmercury concentrations of 0.08 ng/l 

and 0.19 ng/l, allowing a margin of safety of 25% or more, depending on the wildlife species. 

8.4 Seasonal & Inter-annual Variability 

8.4.1 Variability in Aqueous Methyl and Total Mercury 

Mercury loads in Delta tributary inputs fluctuate because of seasonal and inter-annual variation. 

Winter precipitation increases the sediment and total mercury loads entering the Delta through 

erosion and re-suspension of sediment. Most of the total mercury coming from tributaries and 

direct surface runoff enters the Delta during high flow events. In contrast, methylmercury 

production is typically higher during the summer months. In addition, greater total mercury and 

methylmercury loads enter the Delta during wet water years. 

Seasonal and inter-annual variability in methylmercury loads were accounted for in the source 

analysis and methylmercury load allocations by evaluating annual average loads for Delta 

sources and losses for WY2000 to 2003, a relatively dry period that encompasses the available 

concentration data for the major Delta inputs and exports. Twenty-year average, annual loads 

of total mercury were estimated for tributary loads based on flow and precipitation records for 

WY1984-2003. This 20-year period includes a mix of wet and dry years that is statistically 

similar to what has occurred in the Sacramento Basin over the last 100 years. However, 

insufficient data were available at the time the TMDL was developed to estimate 20-year 

average annual loads for methylmercury sources. Methylmercury allocations and total mercury 

limits will be re-evaluated as additional information becomes available. Future monitoring 

programs will accommodate long-term inter-annual variability by evaluating whether sources are 

meeting allocations on a multi-year basis. 

Delta Methylmercury TMDL Report 202 April 2010 

 
8.4.2 Variability in Biota Mercury 

Seasonal and inter-annual variation also occurs in biota. Slotton and others (2003) found that 

Delta species exhibited both seasonal and inter-annual variability in mercury body burden. 

Corbicula (clams) had higher mercury concentrations in the spring while inland silversides 

(representative forage fish species) were higher in fall. In addition, silverside bioaccumulation 

was greater in 1998 than in 1999 and 2000 at many locations in the Delta. Davis and others 

(2002) measured higher mercury concentrations in similar sized largemouth bass in 1999 than 

in 2000. The researchers noted that the winter of 1997 was very wet and speculated that the 

high flows may have introduced significant quantities of “new” mercury that was methylated and 

incorporated into forage fish in 1998. Predacious fish like largemouth bass, which feed upon 

silversides, took an additional year to reflect the higher methylmercury concentrations. 

Seasonal and inter-annual variability in large fish was accounted for in the numeric targets and 

linkage analysis by using data collected over multiple years. Future monitoring will 

accommodate seasonal and inter-annual variability by sampling large fish about every ten 

years. 

8.4.3 Regional and Global Change 

Several ongoing regional and global changes may affect methyl and total mercury loading in the 

Delta. This section identifies several of these. Central Valley Water Board will continue to 

research regional and global changes that may affect efforts to achieve the proposed fish tissue 

targets and incorporate new information and strategies with extensive stakeholder input during 

periodic Delta TMDL control program reviews using an adaptive management approach 

throughout the implementation of the control program. 

8.4.3.1 Population Growth 

The Delta and its tributary watersheds are experiencing substantial population growth. 

Population in the Central Valley increased by about 20% between 1990 and 2000 (AFT, 2006; 

CDOF, 2004). This resulted in the conversion of about 98,000 acres of agricultural land to 

urban uses (AFT, 2006). Four of the five fastest growing cities in the Sacramento Valley are 

located within about one day’s travel time (about 20 to 30 miles by water) of the Delta. The 

California Department of Finance predicts that populations in the Delta/Yolo Bypass counties49

will increase 76% to 213% by 2050 (CDOF, 2007), with an average increase of about 120%. 

Increasing populations will result in increased discharges from municipal wastewater treatment 

plants. In addition, urbanization increases both volume and discharge velocity of runoff 

because of the increase in impervious surfaces. Urbanization also tends to increase pollutant 

loading because impervious surfaces neither absorb water nor remove pollutants, and urban 

development tends to create new anthropogenic mercury pollution sources. As Chapters 6 

and 7 indicate, urban runoff in the Sacramento, Stockton and Tracy areas has higher 

 

49 The CDOF predicts the following population increases by 2050: Contra Costa County - 89%, 

Sacramento County - 76%, San Joaquin County - 213%, Solano County - 105%, and Yolo County - 93% 

(CDOF, 2007). 

Delta Methylmercury TMDL Report 203 April 2010 

 
methylmercury and total mercury concentrations than ambient river concentrations. However, 

little is known about how the conversion of agricultural land to urban uses affects methylmercury 

concentration. 

A study of annual and seasonal trends in atmospheric mercury deposition in Maryland found a 

marked urban influence on mercury deposition; wet depositional fluxes at the urban site were 

two to three times higher than at the rural sites (Mason et al., 2000). The Maryland study 

authors noted that local point sources such as air emissions from waste incinerators and power 

plants may contribute to the mercury deposition at the urban study site. Also, as noted in 

Chapter 4 in the draft Basin Plan Amendment staff report, reactive gaseous mercury (RGM) is 

thought to be emitted primarily from anthropogenic point sources or formed by oxidation 

reactions of gaseous elemental mercury with ozone, hydroxyl radical, nitrate, hydrogen 

peroxide, and/or halogen containing compounds (e.g., Peterson et al., 2009). RGM is more 

likely than other mercury fractions to be converted to methylmercury that is bioaccumulated in 

aquatic food chains (Whalin et al., 2007). Ground-level ozone is a potent irritant that causes 

lung damage and a variety of respiratory problems; ozone is the main component of smog and 

is formed by the reaction of hydrocarbons with nitrogen oxides in the presence of sunlight 

(USEPA OTAQ, 2007). In typical urban areas, a significant fraction of hydrocarbons comes 

from cars, buses, trucks, and nonroad mobile sources such as construction vehicles and boats 

powered by hydrocarbon-based fuels such as gasoline and diesel (USEPA OTAQ, 2007). As a 

result, increasing vehicle exhaust associated with urbanization would lead to increases in the 

hydrocarbon emissions, which subsequently could increase the formation of ground-level ozone 

and the formation of RGM. 

MS4 allocations apply to all urban acreage within MS4 service areas within each Delta subarea 

and apply to the sum of methylmercury loads in existing urban acreage runoff and in runoff from 

future urbanized lands within the MS4 service areas. Staff assumed that, in general, NPDESpermitted municipal WWTP discharges throughout the Delta/Yolo Bypass would increase by 

120%. Staff assumed that half of that growth will be addressed by expansions to existing 

facilities in each Delta subarea, and that half will be serviced by new facilities in each subarea. 

As described in Section 8.1.2 and shown in Tables 8.3 and 8.4, the allocation strategy 

incorporates the assumption that existing municipal WWTPs will increase their discharge 

volumes by 60% and reserves assimilative capacity for new WWTP discharges. 

Chapter 4 in the draft Basin Plan Amendment staff report reviews possible implementation 

strategies to address the methylmercury allocations and total mercury limits for municipal 

WWTP discharges and urban runoff in the Delta region. 

8.4.3.2 Restoration of Wetlands 

Research conducted in the Delta and elsewhere has found that wetlands are efficient sites for 

methylmercury production. There are currently about 26,600 acres of wetlands within the 

Delta/Yolo Bypass (USFWS, 2006). The Record of Decision for the CALFED Bay-Delta 

Program commits it to restore 30,000 to 45,000 acres of fresh, emergent tidal wetlands, 

17,000 acres of fresh, emergent nontidal wetlands, and 28,000 acres of seasonal wetlands in 

the Delta by 2030 (CALFED Bay-Delta Program, 2000a). This is a total of 75,000 to 

90,000 acres of additional seasonal and permanent wetlands in the Delta, which represents 

Delta Methylmercury TMDL Report 204 April 2010 

 
about a three to four times increase in wetland acreage from current conditions. The Bay Delta 

Conservation Plan (BDCP) effort also identifies “priority projects” for near-term implementation 

that may increase the acreage of wetland and seasonally flooded habitat in the Delta (e.g., 

BDCP, 2010). In addition, the newly-established Federal Bay-Delta Leadership Committee’s 

work plan of short-term actions may include expediting habitat restoration projects that are 

ready to move forward, including coordination with BDCP. (Refer to Sections 6.4.8 and 6.4.9 in 

Chapter 6 of the draft Basin Plan Amendment staff report for more information about the BDCP 

and Federal Bay-Delta Leadership Committee.) 

Many of the proposed restoration sites are downstream of mercury-enriched watersheds. 

Marsh restoration efforts below mercury enriched watersheds are proposed for the following 

locations: Yolo Bypass downstream of Cache and Putah Creeks; Dutch Flats downstream of the 

Mount Diablo Mercury mine in the Marsh Creek watershed; and Staten Island and the 

Cosumnes River Wildlife Refuge near the confluence of the Cosumnes River and Mokelumne 

River. 

Mass balance calculations indicated that methylmercury flux from wetland sediments may 

account for approximately 983 g/year of methylmercury (see Table 6.2 in Chapter 6), or about 

19% of the total methylmercury budget for the Delta. A doubling to tripling in methylmercury 

loading from wetland sediments could increase overall Delta loading by about 16 to 27%. The 

linkage relationship suggests that such an increase could result in a 28 to 48% increase in 

mercury concentrations in standard 350-mm largemouth bass (Figure 5.3). CalFed study 

results released since the TMDL was developed indicate that some wetlands may contribute 

less methylmercury loading than assumed for the TMDL calculations, and that some wetlands 

may act as a methylmercury sink. Board staff will continue to track wetland methylmercury 

research and work with wetland managers and other stakeholders to incorporate new 

information into the TMDL control program using an adaptive management approach. 

Chapter 4 in the draft Basin Plan Amendment staff report provides a description of staff’s 

suggested Central Valley Water Board policy for new wetland creation as well as a schedule for 

TMDL and control program reviews, during which the implementation strategy and allocations 

can be modified by the Board as needed to reflect new information. 

8.4.3.3 Water and Flood Management Changes 

As described in Chapter 3, the transport and deposition of mercury-contaminated sediment and 

water management activities contribute to the Delta fish mercury impairment. Several state and 

federal projects affect the transport of mercury and the production and transport of 

methylmercury in the Delta, including but not limited to: 

• Operations to maintain current or future salinity standards in the Delta; 

• Current water deliveries to, diversions from, and storage within the Delta; 

• Yolo Bypass flood conveyance; and 

• Dredging projects throughout the Delta and Yolo Bypass to maintain channel levees for 

flood conveyance, depths of deep water ship channels, and marina depths. 

The source analyses, linkage analysis, methylmercury allocations and total mercury reduction 

requirements described in this TMDL are based on present water management practices and 

Delta Methylmercury TMDL Report 205 April 2010 

 
channel configurations. However, there are several water and flood management projects 

being evaluated by federal and state agencies that have the potential to affect methylmercury 

levels in Delta fish and water, including but not limited to: 

• Water supply reliability projects. Public Policy Institute of California and University of 

California researchers outlined in a 2007 report (Lund et al., 2007) a range of potential 

alternatives for managing the Delta’s water supply that could involve: 

− Maintaining the Delta as a fresh water body, e.g., by maintaining and 

strengthening the current levee system, or strategically focusing levee 

improvements in key areas and allowing lower-reliability levees to fail, which 

would lead to some Delta islands flooding; 

− Allowing the Delta to fluctuate between high and low levels of salinity, e.g., by 

supporting water supply exports with peripheral or through-Delta aqueducts that 

would allow water exports to circumvent the central Delta on their way to the 

lower San Joaquin River or directly to Central Valley Project and State Water 

Project intakes on the southern edge of the Delta, or by creating a major, semiisolated freshwater conveyance corridor by armoring select islands and tidegating selected channels within the central-eastern Delta; or 

− Moving toward a Delta that provides high levels of fresh water as needed, e.g., 

by only allowing exports during times of high discharge of fresh water (generally 

winter and spring), or otherwise managing the Delta to favor key Delta aquatic 

and terrestrial species, which would likely result in fluctuating salinity levels in the 

western Delta and many islands eventually becoming flooded. 

Governor Arnold Schwarzenegger’s Delta Vision process concluded at the end of 2008 

with a suite of strategic recommendations for long-term, sustainable management of the 

Delta. The December 2008 Delta Vision Committee Implementation Report identified 

“fundamental actions” such as: 

− A new system of dual water conveyance through and around the Delta to protect 

beneficial uses of water, with the goal of breaking ground for new conveyance 

improvements in 2011; 

− Additional surface and groundwater storage to allow greater system operational 

flexibility, including surface storage feasibility studies completed for Sites 

Reservoir, Los Vaqueros expansion, and the San Joaquin River Basin; 

− Revision of the San Joaquin River flow objectives by the State Water Board to 

improve Delta water quality, as well as the development and implementation of 

instream flow requirements for the Delta and its tributaries; 

− Strengthen the Delta levee system; and 

− By 2012 develop and implement Total Maximum Daily Load programs for the 

Delta and its tributary areas to eliminate water quality impairments, including but 

not limited to reduction of organic and inorganic mercury entering the Delta from 

tributary watersheds. 

This TMDL report and associated Basin Planning process fulfills the above fundamental 

action of developing and implementing a mercury TMDL for the Delta. However, the 

specific details of the other fundamental actions identified by the Delta Vision Committee 

Delta Methylmercury TMDL Report 206 April 2010 

 
or possible alternatives (e.g., as identified in Lund and others’ 2007 report), and possible 

affects on methylmercury levels in Delta water and fish, are not yet known. 

• The Sacramento Deep Water Ship Channel Deepening Project, which involves dredging 

to deeper depths than done in the past to allow deeper-hulled cargo ships to access the 

Sacramento port. The 2010 Civil Works budget included $10 million for re-launching the 

Sacramento Deep Water Ship Channel deepening project. As noted on a May 2009 Port 

of Sacramento press release, the project would involve deepening the 43-mile ship 

channel connecting the Port of West Sacramento and San Francisco Bay from 30 feet to 

35 feet along its entire length. The channel-deepening project, which was initially started 

in 1989 but later stopped due to since-resolved utility issues, is scheduled to begin in 

2010 with completion targeted for 2013. The federal Civil Works funding would support 

the first phase of construction (Port of West Sacramento, 2009). The project could affect 

conditions within the ship channel as well as entail increased discharges of return water 

with elevated methylmercury concentrations from dredge material disposal areas. (See 

Section 6.2.7 in Chapter 6 for a review of recent return water methylmercury monitoring 

efforts.) 

• Fremont Weir modification to increase flows in the Yolo Bypass. The Blue Ribbon Task 

Force Delta Vision Strategic Plan included the recommendation to increase the 

inundation frequency of the Yolo Bypass to promote primary and secondary productivity 

and splittail spawning by modifying the Fremont Weir. The BDCP has continued to 

forward the concept of lowering a portion of the Fremont Weir and installing an operable 

gate facility (often referred to as creating a “notch” in the weir) to increase periods of Yolo 

Bypass inundation to support native fisheries, particularly splittail and Chinook salmon, 

through managed flow releases down the Bypass (e.g., BDCP, 2009, Table 3.3 

Conservation Measure WOCML2). However, the Lower Yolo Bypass Planning Forum 

identified several concerns, one of which is the potential increases of methylmercury 

(Lower Yolo Bypass Planning Forum, 2008). 

• The San Joaquin River Restoration Program (SJRRP), a comprehensive long-term effort 

to restore flows to the San Joaquin River from Friant Dam to the confluence of Merced 

River. “Interim Flows” began in October 2009. Monitoring is needed to determine how 

increasing flows (and inundation of associated floodplains) will affect methylmercury 

levels in San Joaquin River and Delta water and fish. 

• The South Delta Improvement Project (SDIP), which is intended to mitigate the water 

supply and water quality impacts associated with increasing the maximum allowable 

diversion capacity into Clifton Court Forebay, from which the State Water Project pumps 

its water. The SDIP could entail the construction of a series of permanent barriers that 

would reduce the amount of San Joaquin River flow diverted down Old River towards the 

pumps and away from the San Joaquin River near Stockton. Operation of the permanent 

barriers would control the ratio of San Joaquin to Sacramento River water in much of the 

southern Delta. Sulfate concentrations in the San Joaquin are about seven times higher 

than in the Sacramento River. Therefore, operation of the permanent barriers could exert 

a strong influence on sediment sulfate concentrations in the southern Delta and may 

influence ambient methylmercury levels. (See Section 4.3.12.4 in Chapter 4 of the draft 

Basin Plan Amendment staff report for more discussion on the SDIP.) 

Delta Methylmercury TMDL Report 207 April 2010 

 
To better enable the evaluation and mitigation of negative impacts on water and fish 

methylmercury levels in the Delta from future water and flood management and dredging 

projects, Board staff worked with stakeholders to develop language for the proposed Basin Plan 

amendments included in the draft Basin Plan Amendment report that: 

• Assigns the open water methylmercury allocations jointly to the State Lands Commission, 

the Department of Water Resources, and the Central Valley Flood Protection Board. The 

open water allocations apply to the methylmercury load that fluxes to the water column 

from sediments in open-water habitats within channels and floodplains in the Delta and 

Yolo Bypass. The open water allocations also apply to activities such as water 

management and storage in and upstream of the Delta and Yolo Bypass; maintenance of 

and changes to salinity objectives; dredging and dredge materials disposal, dewatering 

and reuse; and management of flood conveyance flows. 

• Requires State and Federal agencies whose projects affect the transport of mercury and 

the production and transport of methylmercury through the Yolo Bypass and Delta, or 

manage open water areas in the Yolo Bypass and Delta, to conduct methylmercury 

control studies during the first phase of the TMDL implementation period. 

• Requires State and Federal agencies to include requirements for projects under their 

authority to implement methylmercury reductions as necessary to comply with the 

allocations by 2030. 

State and Federal agencies required to participate in the control studies and efforts to reduce 

open water methylmercury include but are not limited to the California Department of Water 

Resources, State Lands Commission, Central Valley Flood Protection Board, State Water 

Resources Control Board, U.S. Army Corps of Engineers, and U.S. Bureau of Reclamation. 

State and federal projects include projects related to flood conveyance, water management, and 

salinity control that have the potential to increase ambient mercury and/or methylmercury levels 

in the Delta or Yolo Bypass. 

Water management activities also affect the residence time of water in the Delta, which affects 

the methylmercury loss rate across the Delta from photodegradation and sediment deposition. 

Changes in water management activities that reduce the methylmercury loss rate across the 

Delta could result in increases in ambient water and fish methylmercury concentrations even if 

the activities do not cause an increase in methylmercury source inputs. The 2003 and 2008 

CalFed studies indicate that loss processes are an important component of the Delta 

methylmercury mass balance and resulting fish methylmercury concentrations in different areas 

of the Delta (see Chapters 3, 5 and 6). It is critical that state and federal agencies evaluate the 

effect of future water management projects on methylmercury loss processes in the Delta 

because (1) the suite of activities that affect production processes may be different from the 

suite of activities that affect loss processes, (2) different agencies may be responsible for these 

different activities, and (3) as a result, tracking activities that affect methylmercury inputs and 

methylmercury loss may provide better direction for a variety of methylmercury control methods. 

The proposed Basin Plan amendment language described in the previous paragraphs was 

purposefully written in way that encompasses activities that affect methylmercury production, 

transport, and loss processes. 

Delta Methylmercury TMDL Report 208 April 2010 

 
Board staff will continue to coordinate with the State and Federal agencies to evaluate the 

potential effects of future water and flood management projects and dredging projects and 

adapt the Delta mercury control program as needed to incorporate new information and control 

strategies during program reviews. 

8.4.3.4 Decreasing Sediment Loads 

The sediment load in the Sacramento River decreased by about 50% between 1957 and 2001 

(Wright and Schoellhamer, 2004). The decrease is believed to be caused by the trapping of 

sediment in reservoirs, a decrease in erodible material from hydraulic mining, changes in land 

use, and construction of levees (Wright and Schoellhamer, 2004; James, 2004). Mercury loads 

are likely to have also decreased during the same period because much of the inorganic 

mercury is transported on sediment particles. It is not known what the magnitude of the 

decrease in mercury loading has been and whether it will continue in the future. The decrease 

in sediment loading suggests that the relative proportion of erodible material from upstream 

watersheds may also be changing. The present 20-year volume-weighted average mercury to 

TSS ratio of sediment entering the Delta is approximately 0.18 mg/kg. This value may change 

depending on the new sources of sediment. The mercury content of surficial sediment is 

important, as it is one of the major factors controlling methylmercury production. Methylmercury 

production in Delta/Yolo Bypass sediment now accounts for about 36% of the methylmercury in 

the Delta (Figure 6.11). It is not clear how this proportion may change in the future. 

8.4.3.5 Climate Change 

Climate change models have predicted several scenarios for global, national and local changes 

that could affect the Delta, including several direct, individual and cumulative impacts. Warmer 

temperatures, water abundance and quality, changes in precipitation patterns, frequency and 

intensity of weather events, and sea level rise are just some of the changes that could impact 

the Delta, its water supply, habitats, and biota (CAT, 2006; CEC, 2006a and 2008; TRNA, 2009; 

Brekke et al., 2004; Knowles and Cayan, 2002; Miller et al., 2003; Service, 2004; Stewart et al., 

2004). In addition to warmer storms, the Sierra Nevada snow pack, California’s largest surface 

“reservoir” has been reducing each year (CAT, 2006; CAPCOA, 2009; TRNA, 2009). Typically, 

snowmelt provides an annual average of 15 million acre feet of water between April and July 

each year (DWR, 2008; TRNA, 2009). Models project the Sierra Nevada snowpack will 

decrease by 25% to 40% by 2050, which would likely result in regions that rely on surface water 

for domestic, industrial, and agricultural supply needing to turn to groundwater or additional 

diversions from the Delta (DWR, 2008; TNRA, 2009). Changes in rainfall and runoff patterns 

combined with warmer temperatures are expected to change the intensity and frequency of 

flood events (CAPCOA, 2009). 

Drier years could result in more frequent and intense wildfires, depleting the carbon storage that 

wildlands and forests provide (CAPCOA, 2009; CAT, 2006; CEC, 2006a and 2006c). Warmer 

temperatures may increase evapotranspiration rates and extend growing seasons, which would 

require more water (CAPCOA, 2009). High frequency flood events will most likely increase, 

changing watershed vegetation and erosion patterns (CAPCOA, 2009; CEC 2006a and 2008). 

Flooding and wildfires would increase sedimentation rates, which would likely negatively affect 

Delta Methylmercury TMDL Report 209 April 2010 

 
reservoir capacity, wildlife habitat and fisheries, and water quality and would likely alter the 

channel shapes and depths in the Delta. Changes in water quality could include changes in 

streamflow patterns, dissolved oxygen, and temperatures; higher turbidity; and concentrated 

pulses of pollutants, all of which could stress fish and increase growth of algae in surface water 

bodies (DWR 2008; TRNA, 2009). Sea level rise is already occurring; the exact rate is unknown 

but it is correlated to the melting rate of the ice sheets on the western Antarctica and Greenland, 

and could result in abrupt changes in sea level conditions (CAT, 2006; CEC, 2006b). Sea level 

rise would likely ultimately result in increased salt water intrusion in the Delta (CEC, 2006a, 

2006d, and 2008; TRNA, 2009). 

Other indirect effects of climate change in California that could affect the Delta, and therefore 

the proposed mercury control program, may include public health impacts; recreational 

availability; changes in growth rates of weeds, pests, and disease; shifts in distribution and 

abundance of biota; and response by biota to elevated carbon dioxide levels (CAT, 2006; 

CAPCOA, 2009; CEC, 2006a). 

The net results of climate change may have unpredictable consequences on ecological 

processes in the Delta including the synthesis and bioaccumulation of methylmercury. The 

source analyses, linkage analysis, methylmercury allocations and total mercury reduction 

requirements described in this TMDL are based on present climate conditions. Staff will reevaluate source analyses and linkage relationships associated with changing environmental 

conditions as more information becomes available in the future. 

8.4.3.6 Global Mercury Emissions 

Because of the complexity of atmospheric mercury sources, and because the Central Valley 

Water Board has limited jurisdiction over these sources, there is greater uncertainty about 

whether these sources can be addressed in a timely manner. Total mercury concentrations in 

precipitation in Oregon and rural northern California are consistently very low and, along with 

Newfoundland, are usually the lowest values in North America (Prestbo and Gay, 2009). 

Atmospheric wet deposition of methylmercury and total mercury directly to the Delta/Yolo 

Bypass makes up only about 1% or less of all methylmercury and total mercury loading to the 

Delta/Yolo Bypass (see Tables 6.2 and 7.1 in the TMDL Report). 

However, a rough estimate of the annual contribution of total mercury from atmospheric wet 

deposition in the tributary watersheds for water year 2001 indicated that wet deposition could 

account for 23 to 69% of the total incoming total mercury load to the Delta (Foe, 2003). In 

addition, recent studies indicate that mercury in atmospheric deposition in northern California 

comes from both local sources (e.g., municipal and industrial emissions, historic mercury and 

gold mine sites, forest fires, and naturally mercury-enriched geologic formations) and sources 

outside of California and the United States (e.g., coal-burning power plants in Asia, gold and 

mercury production, cement production, volcanic emissions, oceans and biomass burning 

(e.g., forest fires and biofuel to produce energy) (e.g., Prestbo and Gay, 2009; Peterson et al, 

2009; Jaffe et al., 2005; Pacyna et al., 2006; Weiss-Penzias et al., 2007; Seigneur et al., 2004; 

Steding and Flegal, 2002; Coolbaugh et al., 2002; Nacht et al., 2004). The largest emissions of 

mercury to the global atmosphere occur from combustion of fossil fuels, mainly coal in utility, 

industrial, and residential boilers; as much as two thirds of the total emission of about 

Delta Methylmercury TMDL Report 210 April 2010 

 
2,190 tons of mercury emitted from all anthropogenic sources worldwide in 2000 came from 

combustion of fossil fuels (Pacyna et al., 2006). 

Key Points 

• Methylmercury allocations are divided among “waste load allocations” for point sources and 

“load allocations” for nonpoint sources. The TMDL is the sum of these components. The 

allocation strategy used in this chapter is based on staff’s recommended strategy described in 

Chapter 4 of the draft Basin Plan Amendment staff report and is designed to remedy the 

beneficial use impairment in all subareas of the Delta. Total mercury limits were developed to 

maintain compliance with the USEPA’s CTR for total mercury in the water column and to 

achieve the San Francisco Bay mercury control program’s total mercury allocation for the 

Central Valley, as well as to help enable methylmercury reductions in Delta water and fish. 

Methylmercury: 

• Methylmercury allocations were made in terms of the existing assimilative capacity of the 

different Delta subareas. The recommended goal for ambient water is an average annual 

concentration of 0.06 ng/l methylmercury in unfiltered water (Chapter 5). This goal describes 

the assimilative capacity of Delta waters in terms of concentration and encompasses a margin 

of safety of approximately 10%. Central Valley Water Board staff anticipates that as the 

average concentration of methylmercury in each Delta subarea decreases to the aqueous goal, 

the targets for fish tissue will be attained. 

• To determine necessary reductions, the existing average aqueous methylmercury levels in 

ambient water in the Delta subareas were compared to the methylmercury goal. The amount of 

reduction needed in each subarea is expressed as a percent of the existing concentration. 

Percent reductions required to meet the goal ranged from 0% in the Central Delta subarea to 

more than 70% in the Yolo Bypass and Marsh Creek subareas. 

Total Mercury: 

• Central Valley Water Board staff recommends that the 110 kg total mercury reduction allocated 

by the San Francisco Bay mercury control program to the Central Valley be met by reductions 

in total mercury entering the Delta from tributary inputs because within-Delta sources comprise 

only a couple percent of total mercury inputs. Initial mercury reduction efforts should focus on 

the watersheds that export the largest volume of highly contaminated sediment. Additional 

reductions may be recommended in future phases of the Delta mercury implementation 

program and upstream control programs to achieve the proposed methylmercury allocations for 

open-water and wetland habitat in the Delta/Yolo Bypass and to address mercury impairments 

in the upstream watersheds. 

Delta Methylmercury TMDL Report 211 April 2010 

 
Options to Consider 

• The methylmercury allocations described in this chapter reflect the preferred implementation 

alternative described in Chapter 4 of the draft Basin Plan Amendment staff report and are 

designed to address the beneficial use impairment in all subareas of the Delta. However, as 

described in the draft Basin Plan Amendment staff report, a number of alternatives are 

possible. The Central Valley Water Board will consider a variety of allocation strategies and 

implementation alternatives as part of the Basin Plan amendment process. 

• Likewise, a variety of total mercury reduction strategies are possible. A total mercury load 

reduction strategy was developed to comply with the San Francisco Bay mercury TMDL 

allocation for to the Central Valley and the USEPA’s criterion for human health protection, 

and to help enable compliance with the proposed methylmercury allocations for open-water 

habitat in the Delta and Yolo Bypass. Staff applied the San Francisco Bay TMDL’s allocated 

reduction of 110 kg total mercury reduction to tributary inputs to the Delta/Yolo Bypass 

because within-Delta sources comprise only a couple percent of total mercury inputs. Initial 

mercury reduction efforts should focus on the watersheds that export the largest volume of 

highly contaminated sediment such as the Cache Creek, Feather River, American River, 

Cosumnes River, and Putah Creek watersheds. Chapter 4 of the draft BPA staff report 

describes additional strategies for minimizing increases from total mercury sources that may 

increase as a result of population growth and regional water management changes. 

Delta Methylmercury TMDL Report 212 April 2010 

 
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Delta Methylmercury TMDL Report A-1 April 2010 

A. WATERWAYS WITHIN THE SACRAMENTO-SAN JOAQUIN DELTA 

This appendix lists the Sacramento-San Joaquin Delta and Yolo Bypass waterways to which 

the proposed TMDL fish tissue targets (a.k.a. water quality objectives for methylmercury in fish) 

apply. These waterways are distinct, readily identifiable water bodies within the boundaries of 

the “legal” Delta (as defined in California Water Code Section 12220) and Yolo Bypass north of 

the Delta that are hydrologically connected by surface water flows (not including pumping) to the 

Sacramento and/or San Joaquin Rivers. Table A.1 lists all the waterways in alphabetical order 

with Yolo Bypass waterways north of the legal Delta boundary listed at the end. Figures A.1 

through A.3 show the locations of the waterways. 

The methylmercury allocations proposed for the Delta methylmercury control program are 

specific to Delta subareas, which are shown on Figure A.4. Table A.2 lists the waterways within 

each of the subareas. 
Delta Methylmercury TMDL Report A-2 April 2010 

Table A.1: Delta and Yolo Bypass Waterways

Map Label # / Waterway Name Map Label # / Waterway Name

1. Alamo Creek 

2. Babel Slough 

3. Barker Slough 

4. Bear Creek 

5. Bear Slough 

6. Beaver Slough 

7. Big Break 

8. Bishop Cut 

9. Black Slough 

10. Broad Slough 

11. Brushy Creek 

12. Burns Cutoff 

13. Cabin Slough 

14. Cache Slough 

15. Calaveras River 

16. Calhoun Cut 

17. Clifton Court Forebay 

18. Columbia Cut 

19. Connection Slough 

20. Cosumnes River 

21. Crocker Cut 

22. Dead Dog Slough 

23. Dead Horse Cut 

24. Deer Creek (Tributary to 

Marsh Creek) 

25. Delta Cross Channel 

26. Disappointment Slough 

27. Discovery Bay 

28. Donlon Island 

29. Doughty Cut 

30. Dry Creek (Marsh Creek tributary) 

31. Dry Creek (Mokelumne River tributary)

32. Duck Slough 

33. Dutch Slough 

34. Elk Slough 

35. Elkhorn Slough 

36. Emerson Slough 

37. Empire Cut 

38. Fabian and Bell Canal 

39. False River 

40. Fisherman's Cut 

41. Fivemile Creek 

42. Fivemile Slough 

43. Fourteenmile Slough 

44. Franks Tract 

45. French Camp Slough 

46. Georgiana Slough 

47. Grant Line Canal 

48. Grizzly Slough 

49. Haas Slough 

50. Hastings Cut 

51. Hog Slough 

52. Holland Cut 

53. Honker Cut 

54. Horseshoe Bend 

55. Indian Slough 

56. Italian Slough 

57. Jackson Slough 

58. Kellogg Creek 

59. Latham Slough 

60. Liberty Cut 

61. Lindsey Slough 

62. Little Connection Slough 

63. Little Franks Tract 

64. Little Mandeville Cut 

65. Little Potato Slough 

66. Little Venice Island 

67. Livermore Yacht Club 

68. Lookout Slough 

69. Lost Slough 

70. Main Canal (Duck Slough tributary) 

71. Main Canal (Italian Slough tributary) 

72. Marsh Creek 

73. Mayberry Cut 

74. Mayberry Slough 

75. Middle River 

76. Mildred Island 

77. Miner Slough 

78. Mokelumne River 

79. Mormon Slough 

80. Morrison Creek 

81. Mosher Slough 

82. Mountain House Creek 

83. North Canal 

84. North Fork Mokelumne River 

85. North Victoria Canal 

86. Old River 

87. Paradise Cut 

88. Piper Slough 

89. Pixley Slough 

90. Potato Slough 

91. Prospect Slough 

92. Red Bridge Slough 

93. Rhode Island 

94. Rock Slough 
Delta Methylmercury TMDL Report A-3 April 2010 

Table A.1: Delta and Yolo Bypass Waterways, Continued

Map Label # / Waterway Name Map Label # / Waterway Name

95. Sacramento Deep Water Channel 

96. Sacramento River 

97. Salmon Slough 

98. San Joaquin River 

99. Sand Creek 

100. Sand Mound Slough 

101. Santa Fe Cut 

102. Sevenmile Slough 

103. Shag Slough 

104. Sheep Slough 

105. Sherman Lake 

106. Short Slough 

107. Smith Canal 

108. Snodgrass Slough 

109. South Fork Mokelumne River 

110. Steamboat Slough 

111. Stockton Deep Water Channel 

112. Stone Lakes 

113. Sugar Cut 

114. Sutter Slough 

115. Sweany Creek 

116. Sycamore Slough 

117. Taylor Slough (Elkhorn Slough 

tributary) 

118. Taylor Slough (near Franks Tract) 

119. Telephone Cut 

120. The Big Ditch 

121. The Meadows Slough 

122. Three River Reach 

123. Threemile Slough 

124. Toe Drain 

125. Tom Paine Slough 

126. Tomato Slough 

127. Trapper Slough 

128. Turner Cut 

129. Ulatis Creek 

130. Upland Canal (Sycamore Slough 

tributary) 

131. Victoria Canal 

132. Walker Slough 

133. Walthall Slough 

134. Washington Cut 

135. Werner Dredger Cut 

136. West Canal 

137. Whiskey Slough 

138. White Slough 

139. Winchester Lake 

140. Woodward Canal 

141. Wright Cut 

142. Yosemite Lake 

143. Yolo Bypass 

144. Deuel Drain 

145. Dredger Cut 

146. Highline Canal 

147. Cache Creek Settling Basin 

Outflow 

148. Knights Landing Ridge Cut 

149. Putah Creek 

150. Tule Canal 
Delta Methylmercury TMDL Report A-4 April 2010 

Figure A.1: Delta Waterways (Northern Panel) 
Delta Methylmercury TMDL Report A-5 April 2010 

Figure A.2: Delta Waterways (Southern Panel) 
Delta Methylmercury TMDL Report A-6 April 2010 

Figure A.3: Northern Yolo Bypass 
Delta Methylmercury TMDL Report A-7 April 2010 

Figure A.4: Subareas for the Delta Methylmercury Control Program 
Delta Methylmercury TMDL Report A-8 April 2010 

Table A.2: Delta and Yolo Bypass Waterways by 

Methylmercury Allocation Subarea 

Waterway Name [Map Label #] Waterway Name [Map Label #] Waterway Name [Map Label #]

CENTRAL DELTA 

Bear Creek [4] 

Bishop Cut [8] 

Black Slough [9] 

Brushy Creek [11] 

Burns Cutoff [12] 

Calaveras River [15] 

Clifton Court Forebay [17] 

Columbia Cut [18] 

Connection Slough [19] 

Dead Dog Slough [22] 

Disappointment Slough [26] 

Discovery Bay [27] 

Dredger Cut [145] 

Empire Cut [37] 

Fabian and Bell Canal [39] 

False River [39] 

Fisherman's Cut [40] 

Fivemile Creek [41] 

Fivemile Slough [42] 

Fourteenmile Slough [43] 

Franks Tract [44] 

Grant Line Canal [47] 

Highline Canal [146] 

Holland Cut [52] 

Honker Cut [53] 

Indian Slough [55] 

Italian Slough [56] 

Jackson Slough [57] 

Kellogg Creek [58] 

Latham Slough [59] 

Little Connection Slough [62] 

Little Franks Tract [63] 

Little Mandeville Cut [64] 

Little Potato Slough [65] 

Little Venice Island [66] 

Livermore Yacht Club [67] 

Main Canal [Indian Slough trib.] [71] 

Middle River [75] 

Mildred Island [76] 

Mokelumne River [78] 

Mormon Slough [79] 

Mosher Slough [81] 

North Canal [83] 

North Victoria Canal [85] 

Old River [86] 

Piper Slough [88] 

Pixley Slough [89] 

Potato Slough [90] 

Rhode Island [93] 

Rock Slough [94] 

San Joaquin River [98] 

Sand Mound Slough [100] 

Santa Fe Cut [101] 

Sevenmile Slough [102] 

Sheep Slough [104] 

Short Slough [106] 

Smith Canal [107] 

Stockton Deep Water Channel [111] 

Taylor Slough [nr Franks Tract] [118] 

Telephone Cut [119] 

Three River Reach [122] 

Threemile Slough [123] 

Tomato Slough [126] 

Trapper Slough [127] 

Turner Cut [128] 

Upland Canal [Sycamore Slough 

tributary] [130] 

Victoria Canal [131] 

Washington Cut [134] 

Werner Dredger Cut [135] 

West Canal [136] 

Whiskey Slough [137] 

White Slough [138] 

Woodward Canal [140] 

Yosemite Lake [142]

MOKELUMNE/COSUMNES RIVERS 

Bear Slough [5] 

Cosumnes River [20] 

Dry Creek [Mokelumne R. trib.] [31] 

Grizzly Slough [48] 

Lost Slough [69] 

Mokelumne River [78]

MARSH CREEK 

Deer Creek [24] 

Dry Creek [Marsh Creek trib.] [30] 

Kellogg Creek [58] 

Main Canal [Indian Slough trib.] [71] 

Marsh Creek [72] 

Rock Slough [94] 

Sand Creek [99]

SACRAMENTO RIVER 

Babel Slough [2] 

Beaver Slough [6] 

Cache Slough [14] 

Dead Horse Cut [23] 

Delta Cross Channel [25] 

Duck Slough [32] 

Elk Slough [34] 

Elkhorn Slough [35] 

Georgiana Slough [46] 

Hog Slough [51] 

Jackson Slough [57] 

Little Potato Slough [65] 

Lost Slough [69] 

Main Canal [Duck Slough trib.] [70] 

Miner Slough [77] 

Mokelumne River [78] 

Morrison Creek [80] 

North Mokelumne River [84] 

Sacramento River [96] 

Snodgrass Slough [108] 

South Mokelumne River [109] 

Steamboat Slough [110] 

Stone Lakes [112] 

Sutter Slough [114] 

Sycamore Slough [116] 

Taylor Slough [Elkhorn Slough 

tributary] [117] 

The Meadows Slough [121] 

Tomato Slough [126] 

Upland Canal [Sycamore Slough 

tributary] [130] 

Winchester Lake [139]
Delta Methylmercury TMDL Report A-9 April 2010 

Table A.2: Delta and Yolo Bypass Waterways by 

Methylmercury Allocation Subarea, Continued 

Waterway Name [Map Label #] Waterway Name [Map Label #] Waterway Name [Map Label #]

SAN JOAQUIN RIVER 

Crocker Cut [21] 

Deuel Drain [144] 

Doughty Cut [29] 

Fabian and Bell Canal [38] 

French Camp Slough [45] 

Grant Line Canal [47] 

Middle River [75] 

Mountain House Creek [82] 

Old River [86] 

Paradise Cut [87] 

Red Bridge Slough [92] 

Salmon Slough [97] 

San Joaquin River [98] 

Sugar Cut [113] 

Tom Paine Slough [125] 

Walker Slough [132] 

Walthall Slough [133]

WEST DELTA 

Big Break [7] 

Broad Slough [10] 

Cabin Slough [13] 

Donlon Island [28] 

Dutch Slough [33] 

Emerson Slough [36] 

False River [39] 

Horseshoe Bend [54] 

Marsh Creek [72] 

Mayberry Cut [73] 

Mayberry Slough [74] 

Rock Slough [94] 

Sacramento River [96] 

San Joaquin River [98] 

Sand Mound Slough [100] 

Sherman Lake [105] 

Taylor Slough [near Franks 

Tract] [118] 

Threemile Slough [123]

YOLO BYPASS-NORTH (a)

Cache Creek Settling Basin 

Outflow [147] 

Knights Landing Ridge Cut [148] 

Toe Drain [124]/Tule Canal [150] 

Putah Creek [149)] 

Sacramento Deep Water Ship 

Channel [95] 

YOLO BYPASS-SOUTH (a)

Alamo Creek [1] 

Babel Slough [2] 

Barker Slough [3] 

Cache Slough [14] 

Calhoun Cut [16] 

Duck Slough [32] 

Haas Slough [49] 

Hastings Cut [50] 

Liberty Cut [60] 

Lindsey Slough [61] 

Lookout Slough [68] 

Miner Slough [77] 

Prospect Slough [91)] 

Sacramento Deep Water Ship 

Channel [95] 

Shag Slough [103] 

Sweany Creek [115] 

Sycamore Slough [116] 

The Big Ditch [120] 

Toe Drain [124] 

Ulatis Creek [129] 

Wright Cut [141]

(a) Both the “Yolo Bypass-North” and “Yolo Bypass-South” subareas contain portions of the Yolo Bypass flood conveyance channel 

shown in Figure IV-4. When flooded, the entire Yolo Bypass is a Delta waterway. When the Yolo Bypass is not flooded, the Toe 

Drain [127] (referred to as Tule Canal [C] for its northern reach), Cache Creek Settling Basin Outflow [A], and Knights Landing Ridge 

Cut [B] are the only waterways within the Yolo Bypass hydrologically connected to the Sacramento River. 
Delta Methylmercury TMDL Report A-10 April 2010

 

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Delta Methylmercury TMDL Report B-1 April 2010 

B. SUMMARY OF FISH MERCURY DATA USED IN TMDL NUMERIC TARGET AND 

LINKAGE ANALYSIS CALCULATIONS 

Section B.1 summarizes the fish mercury data used in the numeric target and linkage analysis 

chapters. Table B.1 lists the fish species and lengths of fish included in the weighted-average1

fish mercury concentrations. Tables B.2 through B.5 list the number of samples and fish 

included in the calculations for each Delta subarea. Data for fish sampled in the Cosumnes 

River and Mokelumne River and in the northern portion of the Yolo Bypass were included in the 

numeric target development calculations. However, only data for fish sampled in the 

Mokelumne River downstream of the Cosumnes River confluence were included in the linkage 

analysis calculations; these data are summarized in Tables B.4 and B.5. All fish data 

summarized in these tables are provided in Appendix K. Section B.3 provides figures that 

illustrate the range of mercury levels in the species within each Delta subarea trophic level food 

group. Appendix C provides a description of the available mercury data for important 

commercial and sport fisheries – such as striped bass, salmon, crayfish, clams and blackfish – 

not included in this data summary because they either do not represent local conditions or do 

not fit within the trophic level food groups defined by the numeric targets. 

 

1

 Weighted average mercury concentration is based on the number of fish in the composite samples analyzed, rather 

than the number of samples. 
Delta Methylmercury TMDL Report B-2 April 2010 

B.1 Description of Fish Mercury DATA Used in the Numeric Target and Linkage 

Analysis Chapters 

Table B.1: Summary of Fish Species & Lengths Used in the Numeric Target & Linkage Analysis 

Chapters

Trophic Level 4 Species & Length Ranges Used for 

Estimation of Human & Bald Eagle Health Risk 

[150-500 mm, unless CDFG minimum catch limit 

applies] (a, b)

Black crappie (> 150 mm) 

Channel catfish (> 200 mm) (b)

Largemouth bass (> 305 mm) (a)

Sacramento pikeminnow (> 150 mm) (b)

Smallmouth bass (> 305 mm) (a)

White catfish (> 200 mm) (b)

White crappie (> 150 mm) (b)

Trophic Level 3 Species & Length Ranges Used for 

Estimation of Human Health and Bald Eagle Risk 

[150-500 mm] (d)

Black bullhead 

Bluegill 

Carp 

Channel catfish (150 - 200 mm) 

Golden shiner 

Goldfish (e)

Redear sunfish 

Sacramento blackfish 

Sacramento splittail 

Sucker 

Unid goby 

White catfish (150 - 200 mm) 

Yellowfin goby 

Trophic Level 3 Species & Length Ranges for 

Estimation of Cormorant, Otter, Mink and Kingfisher 

Health Risk. [All TL3 fish species, 50-150 mm. Small 

individuals of TL4 species of bass, crappie, and catfish, 

are included.] (f)

Bigscale logperch 

Bluegill 

Channel catfish (50 - 150 mm) 

Golden shiner 

Inland silverside 

Largemouth bass (50 - 100 mm) 

Mosquitofish 

Prickly sculpin 

Red shiner 

Redear sunfish 

Shimofuri goby 

Threadfin Shad 

Unid goby 

White catfish (50 - 150 mm) 

White crappie (50 - 120 mm) 

Yellowfin goby 

Trophic Level 4 Species & Length Ranges Used for 

Estimation of Otter and Osprey Health Risk (c)

Black crappie (150 - 350 mm) 

Channel catfish (200 - 350 mm) 

Largemouth bass (150 - 350 mm) 

Sacramento pikeminnow (150 - 350 mm) 

Smallmouth bass (150 - 350 mm) 

White catfish (200 - 350 mm) 

White crappie (150 - 350 mm) 

Trophic Level 3 Species & Length Ranges for 

Estimation of Osprey, Grebe and Merganser Health 

Risk. [All TL3 fish species, 150-350 mm. Small 

individuals of TL4 species of catfish are included.] (c)

Black bullhead 

Bluegill 

Carp 

Channel catfish (150 - 200 mm) 

Golden shiner 

Goldfish 

Redear sunfish 

Sacramento blackfish 

Sacramento splittail 

Sucker 

Threadfin Shad 

Unid goby 

White catfish (150 - 200 mm) 

Yellowfin goby 

Trophic Level 3 for Estimation of Least Tern Health 

Risk. [All TL3 and juveniles of TL4 fish species less 

than 50 mm.] (g)

Bluegill 

Inland silverside 

Mosquitofish 

Prickly sculpin 

Red shiner 

Shimofuri goby 

White catfish 

White crappie 
Delta Methylmercury TMDL Report B-3 April 2010 

TABLE B.1 FOOTNOTES: 

(a) Size minimum based on CDFG fishing regulations: 12 inch minimum (305 mm) for largemouth and smallmouth 

bass. 

(b) Size minimum based on prey type of the fish species. Example: on average, catfish 200 mm and larger are 

mainly piscivorous, meaning that a majority of their diet is trophic level three species. Catfish smaller than 

200 mm eat mainly prey from trophic level 2. Minimum sizes based on length of fish when they become mostly 

piscivorous are given for bass, catfish, pikeminnow and crappie (Source: Moyle PB, 2002. Inland Fishes of 

California, Revised and Expanded, Berkeley, Univ. California Press) 

(c) Size minimum based on prey type of the fish species - see note (b). Maximum size of 350 mm is based on 

largest size generally consumed by osprey or otter. (For bald eagle, use average concentration in TL4 fish 

grouped for humans to assess risk). 

(d) TL3 species for calculating human health risk are those species assumed to be eaten by humans, based on 

general knowledge of the fishery and size of fish. Staff assumes that most fish eaten are at least 150 mm 

(6 inches). Small bass are not included in the trophic level 3 species for human consumption because they 

cannot legally be fished and kept. Crappies are not included because juvenile crappies (TL3) are generally less 

than 120 mm. 

(e) Although goldfish is a TL2 species, large ones may be consumed by humans and are included to estimate 

human risk. Only one Delta goldfish was analyzed for mercury. 

(f) Fish length range of 50-150 mm based on the size of fish typically consumed by kingfisher, cormorant and mink 

(USFWS, 2004). 

(g) Size maximum of 50 mm based on general size limit of prey consumed by California least terns (USFWS, 

2003). 
Delta Methylmercury TMDL Report B-4 

Table B.2: Number of Composite Samples and the Total Number of Fish in the Composite Samples Used to Estimate the 

Trophic Level 3 and 4 Fish Mercury Concentrations for Human and Eagle Health Risk Assessments (a)

Central Delta Cosumnes River Mokelumne R. d/s Cosumnes R. Sacramento River San Joaquin River West Delta Yolo Bypass- North Yolo 

S

Trophic Level (Length 

Range) / Species 

# of 

Samples 

# of 

Fish 

# of 

Samples

# of 

Fish

# of 

Samples 

# of 

Fish 

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish 

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish

# o

Samp

TL4 (150-350 mm) 144 218 16 20 15 21 103 166 95 179 31 39 3 11 52 Channel Catfish 1 4 3 14 1 Crappie 2 9 1 3 2 10 1 Largemouth Bass 102 146 14 18 14 18 52 73 60 92 29 33 1 1 15 Sacramento Pike Minnow 1 3 15 33 1 3 1 3 Smallmouth Bass 1 5 White Catfish 39 59 2 2 35 55 31 70 35 TL3 (150-350 mm) 17 80 4 12 5 17 11 47 12 47 2 9 2 10 5 Black Bullhead 2 9 2 10 Bluegill 6 30 2 10 5 20 4 19 Carp 2 10 4 Redear Sunfish 9 41 1 5 4 20 1 5 Sacramento Blackfish 1 5 Sacramento Splittail 1 4 Sacramento Sucker 3 7 3 7 3 13 1 4 1 White Catfish 3 3 

TOTAL 161 298 20 32 20 38 114 213 107 226 33 48 5 21 57 

(a) Cosumnes River and Yolo Bypass-North fish data were used in the Delta-wide numeric target evaluation (Chapter 3) but not in the linkage analysis b

methylmercury samples were not collected in these subareas. Marsh Creek fish samples collected upstream of any tidal influence, although within thwere not used in any Delta TMDL evaluations because a separate TMDL effort will be conducted for the Marsh Creek watershed. No fish data that mdescribed in Section 4.3.1 were available for the Mokelumne River upstream of the Cosumnes River confluence. 
Delta Methylmercury TMDL Report B-5 

Table B.3: Number of Composite Samples and the Total Number of Fish in the Composite Samples Used to Estimate the W

Trophic Level 3 and 4 Fish Mercury Concentrations for Wildlife Health Risk Assessments (a)

Central Delta Cosumnes River Mokelumne R. d/s Cosumnes R. Sacramento River San Joaquin River West Delta Yolo Bypass- North Yolo 

Trophic Level S

(Length Range) / 

Species 

# of 

Samples 

# of 

Fish 

# of 

Samples 

# of 

Fish

# of 

Samples 

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samp

TL4 (150-350 mm) 100 143 17 17 12 18 78 122 59 117 13 17 2 10 43 Crappie 2 9 1 3 2 10 1 Largemouth Bass 67 83 16 16 11 15 35 47 31 48 11 11 8 Sacramento Pike Minnow 1 3 7 15 1 3 1 3 Smallmouth Bass 1 5 White Catfish 31 51 1 1 35 55 27 66 34 TL3 (150-350 mm) 23 82 2 6 3 11 9 32 10 37 1 5 Black Bullhead 2 9 2 10 Bluegill 5 25 1 5 5 20 3 14 Golden Shiner 1 1 Redear Sunfish 11 43 1 5 3 15 1 5 Sacramento Blackfish 1 5 Sacramento Sucker 1 1 2 6 Threadfin Shad 3 3 Unid Goby 2 2 White Catfish 3 3 Yellowfin Goby 1 1 TL3 (50-150 mm) 193 1391 45 320 9 71 134 711 47 456 66 281 168 Bigscale Logperch 1 12 10 30 1 2 1 3 27 Bluegill 23 74 10 18 1 5 4 16 6 68 3 13 1 Golden Shiner 24 210 3 45 5 31 Largemouth Bass 24 133 1 2 8 81 7 60 5 15 Mosquitofish 1 Prickly Sculpin 1 1 5 Red Shiner 1 1 2 4 1 Redear Sunfish 8 8 1 5 Shimofuri Goby 3 6 1 1 15 Silverside 86 801 32 282 6 62 80 424 18 235 45 189 80 
Delta Methylmercury TMDL Report B-6 

Table B.3: Number of Composite Samples and the Total Number of Fish in the Composite Samples Used to Estimate the W

Trophic Level 3 and 4 Fish Mercury Concentrations for Wildlife Health Risk Assessments (a)

Central Delta Cosumnes River Mokelumne R. d/s Cosumnes R. Sacramento River San Joaquin River West Delta Yolo Bypass- North Yolo 

Trophic Level S

(Length Range) / 

Species 

# of 

Samples 

# of 

Fish 

# of 

Samples 

# of 

Fish

# of 

Samples 

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samples

# of 

Fish

# of 

Samp

Threadfin Shad 20 147 12 70 5 45 1 5 16 Unid Goby 3 3 White Catfish 6 15 White Crappie 3 11 1 1 1 1 1 3 1 2 6 Yellowfin Goby 4 6 1 7 1 2 3 19 1 3 9 53 16 TL3 (<50 mm) 37 201 14 222 2 9 24 124 26 384 22 88 62 Bluegill 17 136 8 78 8 90 11 276 2 6 Mosquitofish 4 17 6 144 2 9 2 7 2 13 5 34 11 Prickly Sculpin 1 1 Red Shiner 11 75 5 Shimofuri Goby 1 3 1 1 3 Silverside 14 43 11 19 2 20 13 37 29 Threadfin Shad 1 4 1 10 13 White Catfish 1 2 White Crappie 1 3 1 

TOTAL 353 1817 78 565 26 109 245 989 142 994 102 391 2 10 273 

(a) Cosumnes River and Yolo Bypass-North fish data were used in the Delta-wide numeric target evaluation (Chapter 3) but not in the linkage analysis be

samples were not collected in these subareas. Marsh Creek fish samples collected upstream of any tidal influence, although within the statutory Delta any Delta TMDL evaluations because a separate TMDL effort will be conducted for the Marsh Creek watershed. No fish data that met the data use ru

were available for the Mokelumne River upstream of the Cosumnes River confluence. 
Delta Methylmercury TMDL Report B-7 April 2010 

B.2 Range of Mercury Levels in Species Present in Each Delta Subarea 

This section provides graphs that show the range of mercury levels in Delta species by trophic 

level, species, and Delta subarea evaluated in the numeric target and linkage analyses: 

• Figure B.1: TL4 Food Group (150-500 mm) Mercury Levels 

• Figure B.2: TL3 Food Group (150-500 mm) Mercury Levels 

• Figure B.3: TL4 Food Group (150-350 mm) Mercury Levels 

• Figure B.4: TL3 Food Group (150-350 mm) Mercury Levels 

• Figure B.5: TL3 Food Group (50-150 mm) Mercury Levels 

• Figure B.6: TL3 Food Group (<50 mm) Mercury Levels 
Delta Methylmercury TMDL Report B-8 April 2010 

 Figure B.1: TL4 Food Group (150-500 mm) Mercury Levels 

Central Delta

0.0

0.4

0.8

1.2

1.6

123456

Mercury Conc. (mg/kg)

Mokelumne River

0.0

0.4

0.8

1.2

1.6

123456

Mercury Conc. (mg/kg)

Yolo Bypass (South)

0.0

0.4

0.8

1.2

1.6

Channel Catfish

Crappie

Largemouth Bass

Sacramento Pike Minnow

Smallmouth Bass

White Catfish

Mercury Conc. (mg/kg)

Sacramento River

0.0

0.4

0.8

1.2

1.6

123456

Mercury Conc. (mg/kg)

San Joaquin River

0.0

0.4

0.8

1.2

1.6

123456

Mercury Conc. (mg/kg)

West Delta

0.0

0.4

0.8

1.2

1.6

Channel Catfish

Crappie

Largemouth Bass

Sacramento Pike Minnow

Smallmouth Bass

White Catfish

Mercury Conc. (mg/kg)
Delta Methylmercury TMDL Report B-9 April 2010 

 Figure B.2: TL3 Food Group (150-500 mm) Mercury Levels 

Central Delta

0.0

0.1

0.2

0.3

0.4

12345678

Mercury Conc. (mg/kg)

Mokelumne River

0.0

0.1

0.2

0.3

0.4

12345678

Mercury Conc. (mg/kg)

Yolo Bypass (South)

0.0

0.1

0.2

0.3

0.4

Black Bullhead

Bluegill

Carp

Redear Sunfish

Sacramento Blackfish

Sacramento Splittail

Sacramento Sucker

White Catfish

Mercury Conc. (mg/kg)

Sacramento River

0.0

0.1

0.2

0.3

0.4

12345678

Mercury Conc. (mg/kg)

San Joaquin River

0.0

0.1

0.2

0.3

0.4

12345678

Mercury Conc. (mg/kg)

West Delta

0.0

0.1

0.2

0.3

0.4

Black Bullhead

Bluegill

Carp

Redear Sunfish

Sacramento Blackfish

Sacramento Splittail

Sacramento Sucker

White Catfish

Mercury Conc. (mg/kg)
Delta Methylmercury TMDL Report B-10 April 2010 

 Figure B.3: TL4 Food Group (150-350 mm) Mercury Levels 

Central Delta

0.0

0.4

0.8

1.2

12345

Mercury Conc. (mg/kg)

Mokelumne River

0.0

0.4

0.8

1.2

12345

Mercury Conc. (mg/kg)

Sacramento River

0.0

0.4

0.8

1.2

12345

Mercury Conc. (mg/kg)

San Joaquin River

0.0

0.4

0.8

1.2

12345

Mercury Conc. (mg/kg)

Yolo Bypass (South)

0.0

0.4

0.8

1.2

Mercury Conc. (mg/kg)

Crappie

Smallmouth Bass

Sacramento Pike Minno

w

Largemouth Bass

Crappie

West Delta

0.0

0.4

0.8

1.2

Mercury Conc. (mg/kg)

Crappie

Smallmouth Bass

Sacramento Pike Minno

w

Largemouth Bass

Crappie
Delta Methylmercury TMDL Report B-11 April 2010 

 Figure B.4: TL3 Food Group (150-350 mm) Mercury Levels

Central Delta

0.00

0.15

0.30

0.45

123456789

10

Mercury Conc. (mg/kg)

Mokelumne River

0.00

0.15

0.30

0.45

123456789

10

Mercury Conc. (mg/kg)

Yolo Bypass (South)

0.00

0.15

0.30

0.45

Black Bullhead

Bluegill

Golden Shiner

Redear Sunfish

Sacramento Blackfish

Sacramento Sucker

Threadfin Shad

Unid Goby

White Catfish

Yellowfin Goby

Mercury Conc. (mg/kg)

No data available for this

trophic level/size category.

Sacramento River

0.00

0.15

0.30

0.45

123456789

10

Mercury Conc. (mg/kg)

San Joaquin River

0.00

0.15

0.30

0.45

123456789

10

Mercury Conc. (mg/kg)

West Delta

0.00

0.15

0.30

0.45

Black Bullhead

Bluegill

Golden Shiner

Redear Sunfish

Sacramento Blackfish

Sacramento Sucker

Threadfin Shad

Unid Goby

White Catfish

Yellowfin Goby

Mercury Conc. (mg/kg)
Delta Methylmercury TMDL Report B-12 April 2010 

 Figure B.5: TL3 Food Group (50-150) Mercury Levels

Central Delta

0.0

0.1

0.2

0.3

13579

1113

Mercury Conc. (mg/kg)

Mokelumne River

0.0

0.1

0.2

0.3

13579

1113

Mercury Conc. (mg/kg)

Yolo Bypass (South)

0.0

0.1

0.2

0.3

Mercury Conc. (mg/kg)

Sacramento River

0.0

0.1

0.2

0.3

13579

1113

Mercury Conc. (mg/kg)

San Joaquin River

0.0

0.1

0.2

0.3

13579

1113

Mercury Conc. (mg/kg)

West Delta

0.0

0.1

0.2

0.3

Mercury Conc. (mg/kg)

Yellowfin Goby

Bluegill

Golden Shiner

Mosquitofish

Prickly Sculpin

Bigscale Logperch

Red Shiner

Redear Sunfish

Shimofuri Goby

White Crappie

White Catfish

Unid Goby

Threadfin Shad

Silverside

Yellowfin Goby

Bluegill

Golden Shiner

Mosquitofish

Prickly Sculpin

Bigscale Logperch

Red Shiner

Redear Sunfish

Shimofuri Goby

White Crappie

White Catfish

Unid Goby

Threadfin Shad

Silverside
Delta Methylmercury TMDL Report B-13 April 2010 

 Figure B.6: TL3 Food Group (<50 mm) Mercury Levels 

Central Delta

0.00

0.05

0.10

0.15

0.20

1234567

Mercury Conc. (mg/kg)

Mokelumne River

0.00

0.05

0.10

0.15

0.20

1234567

Mercury Conc. (mg/kg)

Yolo Bypass (South)

0.00

0.05

0.10

0.15

0.20

Bluegill

Mosquitofish

Prickly Sculpin

Red Shiner

Shimofuri Goby

Silverside

Threadfin Shad

Mercury Conc. (mg/kg)

Sacramento River

0.00

0.05

0.10

0.15

0.20

1234567

Mercury Conc. (mg/kg)

San Joaquin River

0.00

0.05

0.10

0.15

0.20

1234567

Mercury Conc. (mg/kg)g)

West Delta

0.00

0.05

0.10

0.15

0.20

Bluegill

Mosquitofish

Prickly Sculpin

Red Shiner

Shimofuri Goby

Silverside

Threadfin Shad

Mercury Conc. (mg/kg)
Delta Methylmercury TMDL Report B-14 April 2010 

Page intentionally left blank. 
Delta Methylmercury TMDL Report C-1 April 2010 

C. COMMERCIAL AND SPORT FISHING IN THE SACRAMENTO-SAN JOAQUIN DELTA 

As noted in Chapter 2, the Basin Plan lists the existing and potential beneficial uses of the Delta 

and Yolo Bypass. The Yolo Bypass is a 73,300-acre floodplain on the west side of the lower 

Sacramento River. The lower two thirds of the Yolo Bypass are within the legal Delta, and 

waterways within the entire Delta are included in Clean Water Act 303(d) List as mercuryimpaired. However, Table II-1 of the Basin Plan includes separate table rows for the Yolo 

Bypass and Delta. In this appendix, the term “Delta” includes that portion of the Yolo Bypass 

that is within the legal Delta boundary. 

The Basin Plan provides a standard definition for commercial and sport fishing (COMM). The 

COMM designation is defined as “uses of water for commercial or recreational collection of fish, 

shellfish, or other organisms including, but not limited to, uses involving organisms intended for 

human consumption or bait purposes” (CVRWQCB, 2009). The current Basin Plan does not 

include the commercial and sport fishing (COMM) designation for the Sacramento-San Joaquin 

Delta. However, commercial and sport fishing is a past and present use of the Delta. The 

proposed Basin Plan Amendment would add COMM for the Delta as a potential beneficial use, 

as fish in all parts of the Delta are not yet safe to eat in accordance with the proposed fish tissue 

objectives (a.k.a. numeric targets). The Delta provides habitat for as many as forty freshwater, 

saltwater and anadromous fishes (Moyle, 2002). Sport fish species that reside in the Delta 

include striped bass, black bass (e.g., largemouth and smallmouth bass), sturgeon, Chinook 

salmon, American shad, and catfish. 

Fish and other aquatic organisms are collected commercially. CDFG issues commercial fishing 

licenses in California and reports active commercial fishing in the Delta. Detailed historic 

commercial fishing data were not available; CDFG’s Marine Resources website provides 

summary data for commercial landings and associated values for fishing years 2001 and 2002 

(Table C.1). The predominant species targeted include bay shrimp, crayfish and threadfin shad. 

Threadfin shad are used mainly as baitfish for catching striped bass. 

Sport and subsistence fishing is common throughout the Delta and takes place year-round. On 

average, sport fishing license sales in the six Delta counties account for 19% of all licenses 

issued in the State (Table C.2). Although some of these licenses may have been purchased for 

use elsewhere, a survey of anglers indicates similar popularity of the Delta for fishing. The 

Delta Protection Commission and the Department of Parks and Recreation evaluated fishing in 

the Delta by surveying, via mail, adults who purchased fishing licenses in California in 1996 

(DPRec, 1997). Of licensed anglers, 23% reported fishing in the Delta. Delta anglers spent an 

average of 14 days per year fishing. Authors of the survey multiplied the number of anglers that 

use the Delta by the average days spent fishing from boat and shore, and in tournaments. In 

1996, the total of fishing days in the Delta by licensed anglers was 21.6 million. Fishing from 

boat was most popular (11.8 million activity days), followed by fishing from shore (9.6 million 

activity days) and tournament fishing (0.2 million activity days). 

Creel surveys and interviews also provide evidence that sport and subsistence anglers actively 

fish the Delta waterways year-round by boat and from banks. CDFG’s creel surveys indicate 

that a variety of species are caught and kept (Table C.3, Figure C.1). Fishing derbies for striped 
Delta Methylmercury TMDL Report C-2 April 2010 

bass, black bass and sturgeon take place in the Delta annually. The CDHS Environmental 

Health Investigations Branch staff conducted interviews of community-based organizations in 

the Delta region and found that members of many communities regularly eat local fish, 

especially striped bass, catfish, salmon, sturgeon, crappie, and carp (CDHS, 2004). In addition 

to the species listed in Tables C.1 and C.3, Sacramento blackfish and shimofuri goby may also 

be collected from the Delta (Moyle, 2002; anecdotal information). Crayfish are popular with 

some consumers (CDHS, 2006; Silver et al., 2007). Clams are also collected for human 

consumption, particularly by some Hispanic/Latino and Southeast Asians groups (CDHS, 2004; 

2006). A recent fish consumption and advisory awareness survey of low-income women at a 

WIC2

 clinic in Stockton indicated that 32% of the 500 survey participants consumed sport fish, 

29% consumed a combination of commercial and sport fish that exceeded the USEPA/FDA 

national advisory limit,3

 and women who demonstrated advisory awareness and knowledge of 

health-protective behaviors ate less fish overall (Silver et al., 2007). 

Mercury data from Delta sampling efforts (Table C.4) are available for all of the species listed in 

Tables C.1 and C.3 (or for similar species) except hitch, longjaw mudsucker, rainbow and 

steelhead trout, starry flounder, American shad and salmon. Except for American shad and 

salmon, these species do not appear to be key commercial and sport fish in the Delta. To 

evaluate American shad and salmon mercury levels for impairment, data from additional Suisun 

Bay, San Francisco Bay and Delta tributary locations were reviewed. Because salmon are 

anadromous and spend the majority of their lives in the Pacific Ocean, salmon that are caught in 

the Delta will most likely have mercury levels similar to those caught upstream in the tributary 

watersheds. The same is likely true for American shad. Table C.4 includes mercury data for 

American shad and Chinook salmon collected in the Delta and its upstream tributaries. 

Per CDFG fishing regulations, some Delta fish species have size limits: 

• Black bass (e.g., largemouth and smallmouth bass) – minimum 12 inches (305 mm); 

• Striped bass – minimum 18 inches (457 mm); and 

• Sturgeon – between 46 and 72 inches (1,168 to 1,829 mm) 

Only samples collected from the tissue (fillet) of fish that met the size limits for these species 

were included in Table C.4. For other sport fish, only tissue samples collected from fish greater 

than 100 mm were included. Both fillet and whole fish samples were included for all sizes of 

threadfin shad, which is used as bait. In addition, all sizes of crayfish and clams were included. 

Data summarized in Table C.4 were collected between 1970 and 2003. 

The Delta-wide weighted average mercury levels in each species were compared to the USEPA 

criterion for the protection of human health of 0.3 mg/kg and the FDA action level for 

 

2

 Special Supplemental Nutrition program for Women, Infants, and Children (WIC). 3

 The USEPA and FDA recommend that sensitive populations (i.e., women of childbearing age, pregnant and 

breastfeeding women and children) completely avoid consuming high-mercury fish (e.g., shark, swordfish, king 

mackerel, and tilefish) and limited consumption of other commercial fish (12 oz/week, or 48.6 g/day) and sportcaught fish (6 oz/week, or 24.3 g/day). Silver and others attempted to evaluate in their WIC clinic survey whether a 

woman’s combined intake of sport and commercial fish exceeded the USEPA/FDA advisory limits. Because the 

advisory allows women to eat twice as much commercial fish (12 oz) as sport fish (6 oz) in a week, they halved 

each woman’s commercial intake and added it to her sport intake. If this combined amount exceeded 6 oz/week, or 

if the woman ate shark, swordfish, tilefish or king mackerel, she was considered to have exceeded the 

advisory limit. 
Delta Methylmercury TMDL Report C-3 April 2010 

commercially caught fish of 1.0 mg/kg (Figure C.2). Although many individual samples had 

mercury levels that exceeded the FDA action level, none of species-specific weighted average 

mercury concentrations exceeded the action level. In addition, none of the species for which 

commercial fishing licenses were issued exceeded the USEPA criterion. However, the average 

mercury concentrations of several sport fish – sturgeon, catfish, crappie, Sacramento splittail, 

Sacramento pike minnow, largemouth bass, small bass, and striped bass – approached or 

exceeded the USEPA criterion. The bass had the highest average mercury concentrations of 

any species. Largemouth bass had mercury levels comparable to striped bass mercury levels. 

The linkage analyses described in Chapter 5 and fish data described in Appendix B are based 

on samples collected between 1998 and 2001 for species that represent local conditions and fit 

within the trophic level food groups defined by the numeric targets (Chapter 4). All of the 

species listed in Table C.4 and Figure C.1 were addressed by the numeric target development 

and linkage analysis (Chapters 4 and 5, Appendix B), except American shad, Asiatic and 

resident freshwater clams, Chinook salmon, Crangon shrimp, crayfish, striped bass and 

sturgeon. Of these, only striped bass and sturgeon had average mercury concentrations that 

exceeded the USEPA criterion of 0.3 mg/kg. As methyl and total mercury reduction efforts take 

place and the numeric targets are approached throughout the Delta for the species described in 

Appendix B, striped bass and sturgeon data also will be re-evaluated for compliance with the 

USEPA criterion and other adopted, Delta-specific water quality objectives. 

Table C.1: Commercial Fisheries Landings in the Sacramento-San Joaquin Delta and 

Associated Value (a)

Landings (pounds) Value Species 

2001 2002 2001 2002 

Bay shrimp 9,509 9,744 $56,954 $63,149 

Carp 214 $253 

Crayfish 100,008 108,427 $120,403 $114,712 

Hitch 20 $20 

Longjaw mudsucker 29 $0 

Threadfin shad 53,936 49,343 $37,258 $55,028 

Yellowfin goby 285 $24 

TOTAL: 164,001 167,514 $214,912 $232,889 

(a) Source: http://www.dfg.ca.gov/mrd/fishing.html#commercial 
Delta Methylmercury TMDL Report C-4 April 2010 

Table C.2: Average Number of Sport Fishing Licenses Issued in Six Delta Counties (a, b)

County 

Resident Fish 

Licenses Striped Bass Tag Salmon Tag Steelhead Tag 

Alameda 46,240 21,768 429 897 

Contra Costa 42,230 26,948 380 1,039 

Sacramento 89,617 43,260 1,231 6,306 

San Joaquin 43,230 27,906 158 668 

Solano 24,338 19,473 161 469 

Yolo 9,694 4,567 70 293 

Total for Delta Counties: 255,349 143,923 2,427 9,672 

Total for California: 1,356,694 342,638 29,293 56,864 

% Delta Licences: 19% 42% 8% 17% 

(a) Source: http://www.dfg.ca.gov/licensing/statistics/statistics.html 

(b) Resident fish licenses and salmon tags are averaged over a 10-year period, striped bass averaged over 7 years, and 

steelhead averaged over 8 years. 

Table C.3: Sum of Fish Kept by Delta Anglers per the CDFG’s Central Valley 

Angler Surveys for 1999 and 2000. (a)

Species [Acronym Used in Figure C.1] Trophic Level # of Fish Kept 

Catfish [CF] 4 4307 

Striped Bass [SB] 4 2496 

Chinook Salmon 

[a.k.a. king salmon, KS] 3 812 

American Shad [AS] 3 549 

Splittail [SPT] 3 439 

Sunfish [SF] 3 344 

Black Bass [BB] 4 154 

Sturgeon [ST] 3 94 

Starry Flounder [STF] 3 27 

Sacramento Pikeminnow [SPM] 4 22 

Common Carp [CP] 3 20 

Steelhead Trout [SH] 3 7 

Sacramento Sucker [SKR] 3 6 

Rainbow trout [RT] 3 1 

(a) Data obtained from Fraser Shilling (University of California, Davis), who requested the query of 

actual reported number of fish kept and released by species and river mile from the CDFG Creel 

Database for the 1999 and 2000 Central Valley Angler Surveys 1999 and 2000. A summary of 

fish kept by Delta subarea is shown in Figure C.1. 
Delta Methylmercury TMDL Report C-5 April 2010 

Figure C.1: Sum of Fish Kept by Delta Anglers by Delta Subarea per the CDFG’s Central Valley 

Angler Surveys for 1999 and 2000. (Species acronyms are defined in Table C.3.)

TROPHIC LEVEL 3 SPECIES TROPHIC LEVEL 4 SPECIES

Central Delta

Mokelumne/Cosumnes Rivers

Sacramento River

San Joaquin River

West Delta

5 5 10

2

119

0

30

60

90

120

# of Fish Kept

54

1

0

30

60

90

120

# of Fish Kept

549

5 1

221

6 1

439

25 3

757

0

200

400

600

800

# of Fish Kept

10 4

0

30

60

90

120

# of Fish Kept

1

59

22

0

30

60

90

120

AS

CP

KSRT

SF

SH

SKR

SPT

ST

STF

# of Fish Kept

69

1591

436

0

500

1000

1500

2000

# of Fish Kept

2 3

0

5

10

15

20

# of Fish Kept

85

1625

1443

22

0

500

1000

1500

2000

# of Fish Kept

968

73

0

500

1000

1500

2000

# of Fish Kept

121

541

0

500

1000

1500

2000

BB

CF

SB

SPM

# of Fish Kept
Delta Methylmercury TMDL Report C-6 April 2010 

Table C.4: Summary of Available Mercury Concentration Data for Species Targeted by Sport and 

Commercial Fishing (a, b, c)

Common 

# of 

Samples # of Fish 

Min Hg Conc. 

(mg/kg)

Ave Hg Conc. 

(mg/kg)

Max Hg Conc. 

(mg/kg)

Weighted Ave 

(mg/kg)

American Shad 5 18 0.030 0.047 0.066 0.048 

Black Bullhead 4 19 0.053 0.097 0.138 0.099 

Black Crappie 1 6 0.130 0.130 0.130 0.130 

Bluegill 31 135 0.028 0.147 0.418 0.129 

Carp 13 59 0.107 0.235 0.340 0.234 

Catfish 28 28 0.060 0.249 1.180 0.249 

Channel Catfish 28 82 0.060 0.235 0.600 0.291 

Chinook Salmon 10 15 0.040 0.072 0.120 0.062 

Clam, Asiatic 275 717 0.007 0.042 0.195 0.039 

Clam, Resident Freshwater 3 3 0.016 0.035 0.050 0.035 

Crangon Shrimp 10 72 0.006 0.008 0.010 0.008 

Crappie 6 27 0.054 0.296 0.591 0.301 

Crayfish 383 413 0.003 0.191 1.828 0.182 

Largemouth Bass 298 433 0.062 0.585 2.090 0.561 

Redear Sunfish 17 88 0.027 0.106 0.329 0.106 

Sacramento Blackfish 1 5 0.043 0.043 0.043 0.043 

Sacramento Pike Minnow 26 55 0.028 0.572 2.400 0.429 

Sacramento Splittail 1 4 0.370 0.370 0.370 0.370 

Sacramento Sucker 12 43 0.100 0.271 0.492 0.234 

Shimofuri Goby 24 75 0.013 0.034 0.107 0.031 

Smallmouth Bass 1 5 0.570 0.570 0.570 0.570 

Striped Bass 201 245 0.060 0.572 1.850 0.571 

Sturgeon 11 11 0.080 0.271 0.800 0.271 

Threadfin Shad 72 432 0.003 0.038 0.171 0.034 

White Catfish 190 425 0.031 0.343 1.270 0.365 

Yellowfin Goby 2 33 0.040 0.050 0.060 0.048 

(a) CDFG's legal limit is 12 inch minimum (305 mm) for largemouth and smallmouth bass, 18 inch minimum (457 mm) for striped 

bass, and between 46 and 72 inches (1,168 to 1,829 mm) for sturgeon; only data collected from tissue (fillet) samples were 

included. For other sport fish, only tissue samples collected from fish greater than 100 mm were included. Both fillet and whole 

fish samples were included for all sizes of threadfin shad, which is typically used as bait. In addition, all sizes of crayfish and clams 

were included. Results represent total mercury, wet weight concentrations. 

(b) Little-to-no mercury data were available for adult salmon and American shad caught in the Delta. To evaluate salmon mercury 

levels for impairment, data from Suisun Bay and Delta’s tributary watersheds were reviewed. Because salmon are anadromous 

(they spend the majority of their lives in the Pacific Ocean and return to fresh waters only to spawn) adult salmon (typically 

>750 mm) that are caught in the Delta most likely have mercury levels similar to those caught elsewhere in the Bay-Delta and 

tributary watersheds. The same is likely true for American shad. American shad samples were collected from the American 

River, Sacramento River downstream of the Feather River confluence, and Suisun Bay. Chinook salmon samples were collected 

from the upper Sacramento River near Red Bluff, American River, Sacramento River at River Mile 44 and San Francisco Bay. 

(c) Data summarized in this table were collected between 1970 and 2003. In contrast, the numeric target development and linkage 

analyses are based on data collected between 1998 and 2001. 
Delta Methylmercury TMDL Report C-7 April 2010 

Figure C.2: Minimum, Maximum and Weighted Average Mercury Concentrations 

in Species Targeted by Sport and Commercial Fishing Based on Available Data 

0.0

0.5

1.0

1.5

2.0

2.5

Mercury Concentration (mg/kg, w et w eight)

USEPA Criterion (0.3 mg/kg)

FDA Action Level (1.0 mg/kg)
Delta Methylmercury TMDL Report C-8 April 2010 

Page intentionally left blank. 
Delta Methylmercury TMDL Report D-1 April 2010 

D. AVAILABLE AQUEOUS METHYLMERCURY DATA AND POOLED VALUES USED IN 

DELTA LINKAGE & ALTERNATE BAF-BASED LINKAGE APPROACH 

Section D.1 provides tables of methylmercury data, statistical summaries and regressions used 

in the Delta linkage analysis. Section D.2 describes an alternate approach to the linkage 

analysis using site-specific BAFs. 

D. 1 Tables of Methylmercury Data, Statistical Summaries and Regressions Used in the 

Delta Linkage Analysis 

Table D.1: Summary of Available Raw (Unfiltered) Methylmercury Data (ng/l) (a)

Sample Date 

Data 

Source 

Delta 

Mendota 

Canal 

Mokelumne 

River @ I-5 

Sacramento 

River @ 

Freeport 

Sacramento River 

@ Greene's 

Landing 

Sacramento 

River @ 

RM44 

San Joaquin 

River @ 

Vernalis 

State 

Water 

Project X2 

03/28-29/00 A 0.153 0.171 0.148 0.164 0.139 0.204 

04/24/00 A < 0.022 0.28 0.117 0.147 0.0469 0.0819 

05/30/00 A 0.171 0.25 0.336 0.134 0.144 0.241 

06/26/00 A 0.0737 0.114 0.0716 0.22 < 0.022 0.109 

07/18/00 B 0.06 

07/19/00 A < 0.022 < 0.022 0.052 0.118 < 0.022 < 0.022

07/21/00 C 0.052 (b) 

08/16/00 B 0.078 

08/21/00 A < 0.022 0.154 0.11 0.14 < 0.022 < 0.022

09/21/00 C 0.063 

09/26/00 A < 0.022 < 0.022 0.0514 0.0986 0.0581 0.0233 

10/19/00 C 0.071 

10/28-29/00 A < 0.022 0.13 

0.08515 

(FD: 0.0847 & 

0.0856) 

 0.158 < 0.022 < 0.022

11/07/00 B 0.127 0.136 

11/08/00 C 0.099 

12/18/00 A 0.0628 0.0955 0.08905 0.102 0.0501 0.0595 

12/19/00 B 0.108 0.13 

01/17/01 B, C 0.122 0.095 0.119 

01/28-29/01 A 0.144 0.246 0.244 

(FD: 0.24 & 0.248) 0.239 0.113 0.0945 

02/21/01 B, C 0.118 0.077 0.123 

02/26/01 A 0.32 0.1765 0.18 0.0767 0.165 

03/20/01 B 0.168 0.141 

03/21/01 C 0.097 

03/25-26/01 A 0.0924 0.185 

0.08405 

(FD: 0.0825 & 

0.0856) 

 0.178 0.0551 

04/11/01 D 0.07 

04/17/01 B 0.058 0.077 

04/18/01 C 0.076 

04/26/01 D 0.097 

04/29/01 A 0.024 0.201 0.113 0.0934 0.0584 < 0.014

05/15/01 B, D 0.122 0.116 0.153 

05/16/01 D 0.164 
Delta Methylmercury TMDL Report D-2 April 2010 

Table D.1: Summary of Available Raw (Unfiltered) Methylmercury Data (ng/l) (a)

Sample Date 

Data 

Source 

Delta 

Mendota 

Canal 

Mokelumne 

River @ I-5 

Sacramento 

River @ 

Freeport 

Sacramento River 

@ Greene's 

Landing 

Sacramento 

River @ 

RM44 

San Joaquin 

River @ 

Vernalis 

State 

Water 

Project X2 

05/17/01 C 

0.141 

(FD: 0.136 & 

0.146) 

 

05/27-28/01 A 0.0555 0.178 0.0986 0.122 0.0503 0.0409 

05/29/01 D 0.09 

06/06/01 D < 0.02 

06/14/01 D 0.122 

06/19/01 B 0.089 0.18 

06/25-26/01 A 0.0607 0.208 0.0878 0.256 0.0369 

06/28/01 D 0.0878 

07/17/01 B 0.111 0.101 

07/30-31/01 A 0.0645 0.167 0.108 0.147 0.0213 0.0701 

08/14/01 B 0.091 0.097 

08/27/01 A 0.0317 0.065 0.0712 0.194 < 0.014 0.0541 

09/19/01 B 0.073 0.098 

10/01/01 A < 0.014 0.184 0.0953 0.163 0.0321 < 0.014

10/17/01 B 0.072 0.069 

11/14/01 B 0.179 0.143 

12/19/01 B 0.154 0.172 

01/16/02 B 0.202 0.196 

02/05/02 B 0.13 

02/06/02 B 0.083 

03/06/02 B 0.05 0.062 

04/03/02 B 0.052 0.067 

05/08/02 B 0.092 0.107 

06/05/02 B 0.064 0.101 

07/10/02 B 0.144 0.135 

08/07/02 B 0.111 0.108 

09/04/02 B 0.068 0.077 

10/02/02 B 0.081 0.095 

11/06/02 B 0.062 0.076 

12/04/02 B 0.103 0.117 

01/08/03 B 0.111 0.14 

02/05/03 B 0.242 0.251 

02/16/03 B 0.094 

03/05/03 B 0.086 0.081 

03/15/03 B 0.066 

03/18/03 E 

0.1687 

(FD&LR: 0.168, 

0.158, & 0.180) 

 

04/02/03 B 0.089 0.094 

04/15/03 E 

0.122 

(FD: 0.112 & 

0.132) 

 

04/21/03 E 0.1115 

(FD: 0.1 & 0.123) 

04/28/03 E 

0.2605 

(LR: 0.278 & 

0.243) 

 0.146 0.105 0.093 

05/07/03 B 0.12 0.133 
Delta Methylmercury TMDL Report D-3 April 2010 

Table D.1: Summary of Available Raw (Unfiltered) Methylmercury Data (ng/l) (a)

Sample Date 

Data 

Source 

Delta 

Mendota 

Canal 

Mokelumne 

River @ I-5 

Sacramento 

River @ 

Freeport 

Sacramento River 

@ Greene's 

Landing 

Sacramento 

River @ 

RM44 

San Joaquin 

River @ 

Vernalis 

State 

Water 

Project X2 

05/13/03 E 0.122 

05/20/03 E 

0.1002 

(LR: 0.0993 & 

0.101) 

 

05/27/03 E 0.0555 0.0925 0.0824 0.133 0.0759 

06/10/03 E 

0.126 

(FD&LR: 

0.126, 0.143, 

& 0.109) 

 

06/11/03 B 0.1 0.096 

06/18/03 E 0.0366 

06/30/03 E 0.0788 0.178 

0.0291 

(FD&LR: 

0.0345, 

0.0272 & 

0.0256) 

0.0856 

07/01/03 E < 0.0228 0.0233 

07/08/03 E 

0.1845 

(FD: 0.205 & 

0.164) 

 

07/28/03 E 0.0932 0.076 

0.0793 

(FD: 0.0661 & 

0.0924) 

 0.212 0.0284 0.0697 

09/09/03 E 

0.137 

(FD: 0.134 & 

0.140) 

 

09/17/03 E 0.0716 

09/29/03 E 0.0883 0.181 0.058 0.098 

09/30/03 E 0.103 0.0632 

02/19/04 E 0.242 

02/26/04 E 

0.17 

(FD: 0.0642 & 

0.0723) 

 

02/29/04 E 0.126 

(FD: 0.132 & 0.12) 

03/24/04 E 

0.122 

(FD: 0.118 & 

0.126) 

 

03/29/04 E 0.165 

04/12/04 E 0.135 

04/28/04 E 0.0956 

(a) FD: Average of field duplicates. LR: Average of laboratory replicates. Data sources: A – Foe, 2003; B – CMP, 2004; C – SRWP, 

2004; D – Stephenson et al., 2002; E – Data collected by Central Valley Water Board staff to be published in 2008 CALFED report. 

(b) Regional Board staff collected a sample at Greene’s Landing on 19 September 2000 with a value of 0.052 ng/l. Coincidently, the 

SRWP program also collected a sample at Greene’s Landing on 21 September 2000 with a value of 0.052 ng/l. 
Delta Methylmercury TMDL Report D-4 April 2010 

Table D.2: Monthly Average Methylmercury Concentrations (ng/l) for March 2000 to October 2000 Period 

Used to Calculate Average and Median Methylmercury Concentrations for Each Delta 

Subarea. 

Sacramento 

River 

San Joaquin 

River 

Mokelumne 

River 

Central 

Delta 

Western 

Delta 

Month (a) Average 

Conc. 

# of 

Samples 

Average 

Conc. 

# of 

Samples 

Average 

Conc. 

# of 

Samples 

Average 

Conc. 

# of 

Samples 

Average 

Conc. 

# of 

Samples

March 0.148 1 0.164 1 0.171 1 0.146 2 0.204 1 

April 0.117 1 0.147 1 0.280 1 0.029* 2 0.082 1 

May 0.336 1 0.134 1 0.250 1 0.158* 2 0.241 1 

June 0.072 1 0.220 1 0.114 1 0.042 2 0.109 1 

July 0.055 3 0.118 1 0.011* 1 0.011* 2 0.011* 1 

Aug. 0.094 2 0.140 1 0.154 1 0.011* 2 0.011* 1 

Sept. 0.057 2 0.099 1 0.011* 1 0.035* 2 0.023 1 

Oct. 0.078 2 0.158 1 0.130 1 0.011* 2 0.011* 1 

Average 0.120 0.147 0.140 0.055 0.087 

Median 0.086 

13 

0.144 

8 

0.142 

8 

0.032 

16 

0.053 

8 

(a) Monthly averages are the mean of all data collected during a given month. The Central Delta subarea includes data collected at 

the Delta Mendota Canal and State Water Project. The Sacramento subarea includes data collected at Freeport, River Mile 44 

and Greene’s Landing. The raw data are listed in Table D.1. Values with an asterisk were calculated from a water 

concentration that was below detection. Half the detection limit was used in the calculations. 
Delta Methylmercury TMDL Report D-5 April 2010 

Table D.3: Monthly Average Methylmercury Concentrations (ng/l) for March 2000 to April 2004 

Period Used to Calculate Annual Average and Median Methylmercury Concentrations for 

Each Delta Subarea. 

Sacramento 

River 

San Joaquin

River 

Mokelumne 

River 

Central 

Delta 

West 

Delta 

Month (a) Ave. 

Conc. 

# of 

Samples 

Ave. 

Conc.

# of 

Samples

Ave. 

Conc.

# of 

Samples

Ave. 

Conc.

# of 

Samples 

Ave. 

Conc. 

# of 

Samples

January 0.154 8 0.239 1 0.246 1 0.129 2 0.095 1 

February 0.151 11 0.175 2 0.320 1 0.077 1 0.165 1 

March 0.106 12 0.169 3 0.178 2 0.110 4 0.204 1 

April 0.090 14 0.120 5 0.247 3 0.035* 4 0.061* 3 

May 0.133 14 0.128 4 0.174 3 0.095 5 0.119 3 

June 0.087* 12 0.195 4 0.161 2 0.051* 5 0.077 3 

July 0.087 10 0.165 4 0.066* 4 0.038* 6 0.050* 3 

August 0.095 7 0.167 2 0.110 2 0.015* 4 0.033* 2 

September 0.073 9 0.145 4 0.099* 3 0.042* 6 0.043* 3 

October 0.079 6 0.158 1 0.130 1 0.011* 2 0.011* 1 

November 0.117 7 

December 0.125 7 0.102 1 0.096 1 0.056 2 0.060 1 

Annual Average 0.108 0.160 0.166 0.060 0.083 

Annual Median 0.101 

117 

0.165

31 

0.161

23 

0.051

41 

0.061 

22 

(a) Monthly averages are the mean of all data collected during a given month. The Central Delta subarea includes data 

collected at the Delta Mendota Canal and State Water Project. The Sacramento subarea includes data collected at 

Freeport, River Mile 44 and Greene’s Landing. The raw data are listed in Table D.1. Values with an asterisk were 

calculated using one or more samples with concentrations below detection. Refer to Table D.1 for detections limits 

associated with each non-detect value. 
Delta Methylmercury TMDL Report D-6 April 2010 

Figure D.1: Relationships between Standardized 350-mm Largemouth Bass Mercury Levels 

& March 2000 to April 2004 Aqueous Methylmercury. 

The warm and cool seasons are defined as March to October and November to February, respectively.

B. Median Aqueous MeHg

y = 8.0903x1.1926

R2 = 0.86

0.0

0.5

1.0

1.5

0.0 0.1 0.2 0.3

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

A. Average Aqueous MeHg 

y = 14.381x1.51

R2 = 0.88

0.0

0.5

1.0

1.5

0.0 0.1 0.2 0.3

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

Annual Aqueous MeHg vs. LMB MeHg

A. Average Aqueous MeHg

y = 17.795x1.8007

R2 = 0.90

0.0

0.5

1.0

1.5

0.0 0.1 0.2 0.3

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

B. Median Aqueous MeHg

y = 8.8725x1.4347

R2 = 0.92

0.0

0.5

1.0

1.5

0.0 0.1 0.2 0.3

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

Cool Season Aqueous MeHg vs. LMB MeHg

A. Average Aqueous MeHg

y = 11.528x1.339

R2 = 0.83

0.0

0.5

1.0

1.5

0.0 0.1 0.2 0.3

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

B. Median Aqueous MeHg

y = 6.8941x1.0723

R2 = 0.85

0.0

0.5

1.0

1.5

0.0 0.1 0.2 0.3

Aqueous MeHg (ng/l)

Fish MeHg (mg/kg)

Warm Season Aqueous MeHg vs. LMB MeHg
Delta Methylmercury TMDL Report D-7 April 2010 

Table D.4: Monthly Average Filtered Methylmercury Concentrations (ng/l) for March 2000 to October 

2000 Used to Calculate Annual Average and Median Filtered Methylmercury 

Concentrations for Each Delta Subarea. 

Sacramento 

River 

San Joaquin 

River 

Mokelumne 

River 

Central 

Delta 

Western 

Delta 

Month (a) Average 

Conc. 

# of 

Samples 

Average 

Conc. 

# of 

Samples

Average 

Conc. 

# of 

Samples

Average 

Conc. 

# of 

Samples 

Average 

Conc. 

# of 

Samples

March 0.039 1 0.051 1 0.074 1 0.077 2 0.058 1 

April 0.011* 1 0.036 1 0.165 1 0.016* 2 0.011* 1 

May 0.074 1 0.071 1 0.146 1 0.073 2 0.011* 1 

June 0.042 1 - - - 0 0.057 1 0.024* 2 0.031 1 

July 0.022 1 0.011* 1 0.011* 1 0.011* 2 0.011* 1 

August 0.090 1 0.011* 1 0.098 1 0.011* 2 0.011* 1 

September 0.039 2 0.033 1 0.011* 1 0.011* 2 0.011* 1 

October 0.030* 4 0.042 1 0.063 1 0.011* 2 0.011* 1 

Average 0.043 0.037 0.078 0.029 0.019 

Median 0.039 

12 

0.036 

7 

0.069 

8 

0.014 

16 

0.011 

8 

(a) Monthly averages are the mean of all data collected during a given month. The Central Delta subarea includes data 

collected at the Delta Mendota Canal and State Water Project. The Sacramento subarea includes data collected at 

Freeport, River Mile 44 and Greene’s Landing. The raw data are provided in Appendix L. Values noted with an asterisk 

were calculated using one or more water concentrations that were below detection. Half the detection limit was used in the 

calculations. 
Delta Methylmercury TMDL Report D-8 April 2010 

D.2 Alternate BAF-Based Linkage Approach 

The linkage method recommended by Central Valley Water Board staff and described in 

Chapter 5 is based on the statistically significant relationship between standard 350-mm 

largemouth bass and average water methylmercury concentrations. A second approach that 

does not rely on the correlation between largemouth bass and water methylmercury 

concentrations to derive an implementation goal for water makes use of the total 

bioaccumulation factor (BAF), an approach used in numerous USEPA-approved TMDLs across 

the country.4

 A BAF is the ratio of the concentration of a chemical in fish tissue to the 

concentration of the chemical in the water column. As defined in the Mercury Study Report to 

Congress (USEPA, 1997a), the BAF is the concentration of the methylmercury in fish divided by 

the concentration of dissolved methylmercury in water. According to USEPA’s 2003 technical 

support document for the development of national bioaccumulation factors, a total BAF based 

on the total concentration of a chemical in water also can be used. By definition, BAFs imply a 

linear relationship between methylmercury in the water column and in fish. 

Table D.5 lists the BAFs and safe aqueous methylmercury levels calculated for each Delta 

subarea and a Delta-wide BAF using standard 350 mm largemouth bass, average unfiltered 

water methylmercury values, and the following equations. Table D.6 lists BAFs and safe water 

methylmercury levels based on filtered water data. 

Equation 5.1a: 

BAF = LMBMeHgconc ÷ WaterMeHgconc 

Where: WaterMeHgconc = Water column concentration of unfiltered MMHg (μg/L)

 LMBMeHgconc = 350-mm LMB tissue concentration (μg/kg) 

Equation 5.b: 

Safe Level for Water = LMBMeHg Proposed Goal ÷ BAF 

Where: LMBMeHgconc = Proposed implementation goal for 350-mm LMB (μg/kg) 

Using “Delta-wide” values from Table 5.3 as an example: 

BAF = (0.59 mg/kg x 1000) ÷ (0.110 ng/l ÷ 1000) 

 = 5.35 x 106

Safe Level for Water = (0.180 ÷ 5.35 x 106

) ÷ 106 

 = 0.034 ng/l 

The safe aqueous methylmercury concentrations produced by the BAF method are slightly less 

than but comparable to the safe levels produced using the regression-based approach. This 

similarity most likely occurs because both methods used the same data, and because the 

regressions are nearly linear at low fish and water methylmercury levels. However, the 

regression-based method is preferred because it does not inherently assume a linear 

relationship between fish and water methylmercury levels. 

 

4

 Refer to: http://www.epa.gov/OWOW/tmdl/index.html. 
Delta Methylmercury TMDL Report D-9 April 2010 

Table D.5: Delta BAFs and Corresponding Safe Methylmercury Levels in Water Calculated Using 

Unfiltered Water 

Delta Subarea 

Sacramento 

River 

Mokelumne 

River 

Central 

Delta 

San Joaquin 

River West Delta 

DeltaWide (a)

Standardized 350-mm 

Largemouth Bass MeHg (mg/kg) 0.72 1.04 0.19 0.68 0.31 0.59 

March-October 2000 Average 

MeHg in Unfiltered Water (ng/l) 0.120 0.140 0.055 0.147 0.087 0.110 

BAF 6.00 x 106 7.43 x 106 3.45 x 106 4.63 x 106 3.56 x 106 5.35 x 106

Safe Methylmercury 

Concentration in Water (b) 0.030 0.024 0.052 0.039 0.051 0.034 

(a) Delta-wide largemouth bass and water methylmercury concentrations were estimated by averaging the subarea values. 

The Delta-wide BAF and safe water concentration were calculated using the Delta-wide largemouth bass and water values. 

(b) Safe levels in water correspond to the proposed implementation goal of 0.18 mg/kg methylmercury in standard 350-mm 

largemouth bass. 

Table D.6: Delta BAFs and Corresponding Safe Methylmercury Levels in Water Calculated Using Filtered 

Water Data 

Delta Subarea 

Sacramento 

River 

Mokelumne 

River 

Central 

Delta 

San Joaquin 

River West Delta 

DeltaWide (a)

Standardized 350-mm 

Largemouth Bass MeHg (mg/kg) 0.72 1.04 0.19 0.68 0.31 0.59 

March-October 2000 Average 

MeHg in Filtered Water (ng/l) 0.043 0.078 0.029 0.037 0.019 0.041 

BAF 1.67 x 107 1.33 x 107 6.55 x 107 1.84 x 107 1.63 x 107 1.43 x 107

Safe Methylmercury 

Concentration in Water (b) 0.011 0.014 0.027 0.010 0.011 0.013 

(a) Delta-wide largemouth bass and water methylmercury concentrations were estimated by averaging the subarea values. The 

Delta-wide BAF and safe water concentration were calculated using the Delta-wide largemouth bass and water values. 

(b) Safe levels in water correspond to the proposed implementation goal of 0.18 mg/kg methylmercury in standard 350-mm 

largemouth bass. 
Delta Methylmercury TMDL Report D-10 April 2010 

Page intentionally left blank. 
Delta Methylmercury TMDL Report E-1 April 2010 

E. METHODS USED TO ESTIMATE WATER VOLUMES FOR DELTA 

AND SACRAMENTO BASIN INPUTS AND EXPORTS 

Average annual water volume is a critical component of the source assessments described in 

Chapters 6 and 7 because water volume is multiplied by the concentration of each constituent 

to determine loads. Also, a balanced water budget indicates that all major water imports and 

exports have been identified. This appendix contains a hydrologic evaluation of wet and dry 

years during the methyl and total mercury source assessment study periods (Section E.1) and a 

description of methods used to estimate water volumes used in the source assessments 

(Section E.2). All figures and tables referenced in the text are provided at the end of 

Appendix E. 

E.1 Hydrologic Evaluation of Source Assessment Study Periods 

Water volumes entering the Delta vary from season to season and year to year. A “water year” 

(WY) is the period between October and September that encompasses the entire wet season; 

for example, WY2001 is the period between 1 October 2000 and 30 September 2001. The 

methylmercury load analyses (Chapter 6) focused on the four-year WY2000-2003 period, which 

encompasses the available methylmercury concentration data at the time the TMDL was 

developed. The total mercury and sediment load analyses (Chapter 7) focused on two periods, 

WY2000-2003 and WY1984-2003. The WY2000-2003 period was selected for comparison to 

the methylmercury load estimates. Enough information was available to evaluate the twentyyear WY1984-2003 period for the Sacramento Basin tributaries, which input the most total 

mercury to the Delta of any source. This period was evaluated because it includes a fairly even 

mix of wet and dry years and better describes long-term average conditions. 

Water year types in California are classified according to the natural water production of the 

major basins. The California Department of Water Resources (DWR) Hydrologic Classification 

Index (HCI) was used to evaluate the distribution of wet and dry years in the Central Valley. 

Figure E.1 graphs the Sacramento Valley and San Joaquin Valley indices for the period of 

record (1901 to 2003). The DWR HCI classifies water years as “wet”, “above normal”, “below 

normal”, “dry”, or “critical dry” (DWR, 2003). For the Sacramento Valley, normal hydrologic 

conditions equate to an index value of 7.8, wet is ≥9.2, dry is 5.4 to 6.5, and critical dry is ≤5.4. 

For the San Joaquin Valley, normal hydrologic conditions equate to an index value of 3.1, wet is 

≥3.8, dry is 2.1 to 2.5, and critical dry is ≤2.1. The WY2000-2003 period has average indices of 

7.3 and 2.7 for the Sacramento and San Joaquin watersheds, respectively, and appears to be a 

relatively dry period compared to the period of record. In comparison, the WY1984-2003 period 

appears to encompass a fairly even mix of wet and dry years. The Sacramento River HCI 

indicates that during the WY1984-2003 period, ten water years were “wet” or “above normal”, 

and ten years were “below normal,” “dry,” or “critical dry”. The San Joaquin River HCI indicates 

that nine water years were “wet” or “above normal”, and eleven years were “below normal,” 

“dry,” or “critical dry.” 
Delta Methylmercury TMDL Report E-2 April 2010 

The distribution of wet/dry years in the twenty-year study period was compared to the 

distribution of wet/dry years during the past century in the Sacramento and San Joaquin River 

watersheds. The Sacramento River index includes water years 1906 to 2003 and the San 

Joaquin River index includes water years 1901 to 2003. Using the Chi-square test, it was 

determined that the distribution of water year classifications between the WY1984-2003 period 

and the entire record was not statistically different (a=0.05) from the distributions for both the 

Sacramento and San Joaquin River watersheds. Therefore, it was concluded that the WY1984-

2003 period is representative of long-term conditions. 

E.2 Water Volume Estimation Methods 

Average annual water volumes were estimated for the following Delta inputs and exports: 

1. Tributary inputs to the Delta; 

2. Wastewater treatment plants; 

3. Atmospheric deposition; 

4. Urban runoff; 

5. Delta outflows to San Francisco Bay and diversions to southern California (Delta 

Mendota Canal and State Water Project); 

6. Agricultural diversions; 

7. Evaporation; and 

8. Dredging. 

The WY2000-2003 period is a relatively dry four-year period, while the WY1984-2003 period 

reflects an even mix of wet and dry years, conditions typical for the last 100 years. As illustrated 

by Table 6.1 in Chapter 6, the WY2000-2003 water budget balances within 5% and the 

WY1984-2003 water budget balances within 1%. This indicates that the major water inputs and 

exports have been identified. 

Water volume information was obtained from a variety of sources (Table E.1). A DWR model, 

Dayflow, provided daily flow estimates for several of the major Delta exports, including outflow 

to San Francisco Bay, the Delta Mendota Canal (DMC), State Water Project (SWP), and 

agricultural withdrawals. Four-year and 20-year precipitation amounts and land use acreages 

were used to estimate wet weather inputs from urban areas, atmospheric deposition, and 

tributaries with no flow gages, whenever that duration of data was available for a given 

monitoring station. Project files were reviewed to determine recent average annual discharges 

from NPDDES-permitted facilities in the Delta and annual average volumes removed by 

dredging projects. The following sections describe how each water volume was derived. 

E.2.1 Flow-Gage Based Water Volumes

Average annual water volumes were estimated for tributary inputs to the Delta using a variety of 

methods determined by available data (Table E.1). Flow gages provided daily flows for the 

major tributaries. If there was no nearby flow gage, Staff used precipitation-based runoff 

estimates to calculate loads (Section E.2.3). 
Delta Methylmercury TMDL Report E-3 April 2010 

Table E.2 lists the flow gages used to calculate average annual water volume. The use of 

multiple flow gages was required to estimate water volumes corresponding to the following 

monitoring locations: Feather River near Nicolaus, Mokelumne River downstream of I-5, and 

Yolo Bypass. Because of the complexities of the Yolo bypass hydrology, it is discussed in its 

own section (Section E.2.2). 

Staff estimated flows for the Feather River at Nicolaus using the formula: 1.11 x [Bear at 

Wheatland + Yuba at Marysville + Feather at Gridley]. The coefficient of 1.11 was determined 

by fitting a regression of historical flow data at Nicolaus when flows were rated (1942 to 1983) 

and historical flow data for the same time period paired by date of the sum of Feather River at 

Gridley, Yuba River at Marysville and the Bear River at Wheatland. The coefficient of 1.11 

compensates for inputs not included by the Gridley, Marysville, and Wheatland gages. 

The flow of the Mokelumne River near I-5 was estimated by summing the gaged flows of the 

Mokelumne at Woodbridge and Cosumnes River at Michigan Bar. If Mokelumne at Woodbridge 

flows were missing for particular days, the sum of Camanche Dam outflow and Cosumnes River 

at Michigan Bar was used. If both the Mokelumne at Woodbridge flow and Camanche Dam 

outflow were missing, then those particular days were considered missing values. Flow records 

for Mokelumne at Woodbridge flow and Camanche Dam outflow for water years 1995 and 1996 

were missing more than 20% of their values; all other water years during the study period had 

either Mokelumne at Woodbridge flow and/or Camanche Dam outflow records available. 

Therefore, the 20-year flow average was estimated by normalizing the total flows for the 

WY1984-2003 period. To estimate the missing values, first the number of days in the 20-year 

period (7305) was divided by the number of days with a recorded value in the flow record 

(6517). Then the resulting quotient was multiplied by the calculated sum of loads divided by 20 

to obtain the average annual load. Normalization was not needed for the WY2000-2003 period. 

E.2.2 Yolo Bypass Inflows & Outflows to the Delta & Hydrologic Conditions in January 1995

Yolo Bypass Boundary Definition & Hydrologic Features 

The Yolo Bypass is a 73,300-acre floodplain on the west side of the lower Sacramento River in 

Yolo and Solano Counties (Figure E.2) within the levees of the Sacramento River Flood Control 

Project. The Fremont and Sacramento Weirs route floodwaters to the Yolo Bypass from the 

Sacramento and Feather Rivers, Sutter Bypass and their associated tributary watersheds. 

Cache and Putah Creeks, Willow Slough, and the Knights Landing Ridge Cut from the Colusa 

Basin all drain directly to the Yolo Bypass. 

The Interstate 80 (I-80) causeway bisects the Yolo Bypass east to west. The bypass north of 

I-80 is bounded on the east by the Tule Canal (the upper extension of the Toe Drain) and the 

East Bypass Levee and bounded on the west by the West Bypass Levee. For the purpose of 

this TMDL, staff used the boundaries defined by 2001 Yolo Basin Foundation report, 
Delta Methylmercury TMDL Report E-4 April 2010 

A Framework for the Future: Yolo Bypass Management Strategy (Jones & Stokes, 20015) to 

delineate the bypass south of I-80. South of I-80 the bypass is bounded on the east by the Toe 

Drain and the East Bypass Levee (also considered the west levee of the Sacramento River 

Deep Water Ship Channel), downstream to the northwest corner of Prospect Island. At this 

location, the bypass extends east to include Prospect Island, although the East Bypass Levee 

remains intact along the west edge of the island. South of Prospect Island, the east side of the 

Bypass extends downstream of the confluence of Cache and Lindsey Sloughs to the 

downstream boundary of Egbert Tract. This eastern downstream limit of the bypass is roughly 

co-located with the confluence of Steamboat and Cache Sloughs. The west side of the bypass 

is bounded by the West Bypass Levee to just south of Putah Creek and the Putah Creek Sink 

downstream of Putah Creek. The southern bypass is unleveed on the west side for 

approximately eight miles, allowing floodwaters to flow unimpeded as far west as Yolo County 

Road (CR) 104. Farther downstream (approximately 1 mile north of Yolo CR 155), the West 

Bypass Levee resumes and extends south and west of Liberty Island. The west side of the 

bypass extends farther south, downstream of Liberty Island, and along the western boundary of 

Egbert Tract. 

The southern portion of the Yolo Bypass (about 52,600 acres) lies within the statutory Delta 

boundary and has some tidally influenced areas. Tidal conditions are observed as far upstream 

in the Toe Drain as the I-80 causeway (Jones & Stokes, 2001). The Toe Drain, which drains to 

Prospect Slough, is the primary drainage in the Yolo Bypass. The water elevation in the Toe 

Drain typically fluctuates tidally between three and seven feet at the Yolo Bypass at Lisbon gage 

(operated by DWR, gage ID “LIS”) (Figure E.2). A few hundred feet north of this gage, the 

Lisbon Weir limits the range of tidal fluctuation upstream of the weir. The main part of the weir 

consists of a sheet piling-reinforced rock mound with three “slap gates” (like trap doors) that 

allow water to flow northward with incoming tides, but not southward with outgoing tides (Jones 

& Stokes, 2001; Kirkland, personal communication). The weir impounds upstream inflow and 

tidal water at an elevation equal to the weir crest elevation (2.5 feet above sea level) (Jones & 

Stokes, 2001). This provides higher and more stable water levels for upstream agricultural 

diversion pumps. 

When tributary inputs upstream of Lisbon Weir are greater than approximately 800 cfs, water 

flows southward over the weir (Kirkland, personal communication). During the summer season, 

the water stage is typically greater to the south of the weir, so that there is a net upstream flow 

on Toe Drain. However, even during the summer, very high tides cause the pool upstream of 

the weir to fill and then drain southward across the top of the weir when the tide turns (Kirkland, 

personal communication). Until recently, the Lisbon gage provided only stage information; it 

was rated for velocity in winter 2004. Preliminary calculations by DWR and Central Valley 

Water Board staff indicate that there was a monthly net downstream flow from the Yolo Bypass 

at Lisbon ranging between 56,00 and 152,000 acre-feet per month for the months of March, 

April and May 2004. However, there was a net upstream flow of 700 to 3,000 acre-feet per 

month in June and July 2004. That is, there was no net outflow from the Yolo Bypass to the 

Delta during these summer months. Observations during summer months in 2005 and 2006 

 

5

 Jones & Stokes. 2001. A Framework for the Future: Yolo Bypass Management Strategy. Final report (J&S 99079) 

prepared for the CALFED Bay-Delta Program by the Yolo Bypass Working Group, Yolo Basin Foundation, and 

Jones & Stokes. August 2001. 
Delta Methylmercury TMDL Report E-5 April 2010 

indicate there is net outflow from the Yolo Bypass during wetter years (Foe, personal 

communication). 

Yolo Bypass Inflow and Outflow Calculations 

Aqueous methyl and total mercury sampling took place on Prospect Slough at the Toe Drain to 

estimate mercury concentrations in outflows from the Yolo Bypass to the central Delta. 

However, no flow gage is available at that location. Several gages are available upstream that 

can be used to estimate Yolo Bypass outflows. The “Yolo Bypass near Woodland” flow gage 

(USGS gage 11453000) represents the sum of inflow from Fremont Weir, Knights Landing 

Ridge Cut, and Cache Creek Settling Basin (Figure E.2); the USGS Woodland gage record 

includes only daily mean flows greater than 1,000 cfs. Flow gages are also active on Cache 

Creek at Yolo (USGS gage 11452500), Sacramento Weir (USGS gage 11426000), Putah Creek 

near Winters (USGS gage 11454000), and the Putah South Canal (USGS gage 11454210, 

available after 10/1/94), which diverts water from Putah Creek downstream of the Winters gage. 

No flow gages are active on Knights Landing Ridge Cut or Willow Slough Bypass and, as noted 

above, the gage on Toe Drain near Lisbon was only recently rated for velocity. Inflows from 

Knights Landing Ridge Cut, Putah Creek and Willow Slough to the Yolo Bypass were estimated 

using hydrologic models developed by Jones and Stokes (Jones & Stokes, 2001). 

Knights Landing Ridge Cut. The Knights Landing Ridge Cut (KLRC) is an artificial overflow 

channel that connects the lower end of the Colusa Basin Drain (CBD) to the Yolo Bypass. 

Under low-flow conditions, the CBD discharges to the Sacramento River through a set of gates, 

and little to no water flows from the KLRC to the Yolo Bypass (Jones & Stokes, 2001). The 

daily discharge of the CBD to the Sacramento River is measured by a gage operated by DWR 

(Colusa Basin Drain at Knights Landing). However, when the Sacramento River stage exceeds 

25 feet, the gates close and flow in the CBD is shunted through the KLRC to the Yolo Bypass 

(Jones & Stokes, 2001). These flows are not gaged; however, staff was able to estimate the 

KLRC inflows to the Yolo Bypass using a hydrologic model developed by the consulting firm, 

Jones and Stokes. 

The daily discharge velocity of the CBD is measured by a gage operated by DWR at a location 

near Highway 20. The CBD near Highway 20 gage is about 20 miles upstream of the 

confluence between the CBD and the KLRC. Therefore, the gage flows do not include the 

runoff from 22 square miles of tributary watershed area to the CBD between the Highway 20 

gage and the CBD-KLRC confluence (Jones & Stokes, 2001). According to the Jones & 

Stokes hydrologic model, during significant rainfall events (days with greater than 0.3 inches of 

rain at Colusa), the total flow arriving at the lower end of the CBD was estimated by multiplying 

the gaged daily flow at CBD near Highway 20 by the drainage area ratio of 1.21. Daily 

precipitation data at Colusa was obtained from a gage operated by the California Irrigation 

Management Information System. During days with no significant rainfall (less than 

0.3 inches/day of rain at Colusa), the total flow at the lower end of the CBD was estimated to be 

equal to the CBD near Highway 20 gaged daily flow. 

Greater than 0.3 inches of rain at Colusa: 

QCBD = 1.21QCBD20 
Delta Methylmercury TMDL Report E-6 April 2010 

Less than 0.3 inches of rain at Colusa: 

QCBD = QCBD20

Where: QCBD20 = Gaged flow of the Colusa Basin Drain at Highway 20 

QCBD = Estimated total flow arriving at the lower end of the Colusa Basin Drain 

Because the majority of the water from the CBD arriving at the Knights Landing Ridge Cut is 

discharged to the Sacramento River, the estimated KLRC inflow to the Yolo Bypass was then 

calculated by subtracting the gaged outflow to the Sacramento River (the CBD at Knights 

Landing DWR gage) from the estimated total flow arriving at the lower end of the drain (Jones & 

Stokes, 2001): 

QYB = QCBD – QKNL 

Where: QYB = Knights Landing Ridge Cut inflow to the Yolo Bypass 

QKNL = Gaged outflow to the Sacramento River from the Knights Landing Ridge Cut 

Putah Creek. Upstream of the Yolo Bypass, Putah Creek is impounded by the Monticello Dam, 

a large dam that creates Lake Berryessa, and the Putah Diversion Dam, a small rediversion 

dam that creates Lake Solano. The Putah Diversion Dam is about 7 miles downstream of the 

Monticello Dam. Much of the water trapped behind the Putah Diversion Dam is pumped 

southward through the Putah South Canal for agricultural uses. However, some of the water in 

Lake Solano is released to the lower Putah Creek channel. These releases to Putah Creek are 

gaged by USBR. However, the Putah Diversion Dam is located about 22 miles upstream of the 

West Bypass Levee of the Yolo Bypass. Flows between the Putah Diversion Dam and the Yolo 

Bypass are affected by seepage losses, tributary inflows, evapotranspiration, and channel 

storage (Jones & Stokes, 2001). 

Staff estimated the Putah Creek inflows to the Yolo Bypass using the hydrologic model 

developed by Jones and Stokes (Jones & Stokes, 2001). The calculations were divided into 

three hydrologic conditions: scheduled Berryessa and Putah Diversion Dam water-rights 

releases only, active rainfall runoff, and Lake Berryessa spills. During periods when flows at 

Putah Diversion Dam consisted entirely of scheduled water-rights releases, inflow to the Yolo 

Bypass equals the Diversion Dam releases minus the net flow losses along the channel. During 

periods when there was active rainfall runoff but no spill from Lake Berryessa, inflow to the Yolo 

Bypass equals two times the gaged flow at Putah Diversion Dam minus net flow losses. When 

Lake Berryessa was spilling, inflow to the Yolo Bypass equals the gaged flow at Putah Diversion 

Dam minus net flow losses. The net flow losses along the 22 miles downstream of the 

Diversion Dam were estimated to be a constant 30 cfs in the Jones & Stokes model. The 

equations for the flow model are as follows: 

Conditions 1 (scheduled releases only) and 3 (Lake Berryessa spill): 

QYB = QPDD – 30 

Condition 2 (active rainfall runoff): 

 If: 1. QPDD > 60 cfs (to eliminate scheduled release-only condition) 

 2. QBER < 900 cfs (to eliminate Lake Berryessa spill periods) 

 3. QINT > 100 cfs (to eliminate noise in the interdam runoff estimates) 
Delta Methylmercury TMDL Report E-7 April 2010 

 Then: QYB = QPDD(2) - 30 

Where: QPDD = Putah Creek flow at Putah Diversion Dam 

 QBER = Outflow from Lake Berryessa (releases plus spills from USBR gage) 

 QINT = Rainfall runoff from the reach between Lake Berryessa and Putah 

Diversion Dam 

 QINT = QINF - QBER (QINF = estimated inflow to Lake Solano calculated by USBR) 

 QYB = Putah Creek outflow to Bypass 

Willow Slough. Flows in Willow Slough were not gaged at any time during the study period. 

Staff estimated the Willow Slough inflows to the Yolo Bypass using a hydrologic model 

developed by Jones and Stokes (Jones & Stokes, 2001). This model estimated Willow Slough 

daily inflows to the Yolo Bypass by correlation with gaged runoff in the interdam reach of Putah 

Creek, adjusted for drainage area size. Runoff in the interdam reach of Putah Creek was 

calculated by subtracting gaged Lake Berryessa outflow (USBR gage BER) from the Lake 

Solano inflow (calculated by USBR from a daily water balance). The following equation was 

used to calculate the estimated Willow Slough inflow to the Yolo Bypass: 

QWS = -0.000423(QINT)

2

 + 3.19QINT 

Where: QWS = Willow Slough outflow to the Bypass 

 QINT = Rainfall runoff from the interdam reach between Lake Berryessa and 

Putah Diversion Dam 

Yolo Bypass Inflows. To estimate total inflows to the Yolo Bypass upstream of Prospect Slough 

at Toe Drain on the days that average daily flows were greater than 1,000 cfs at Yolo Bypass 

near Woodland, the following equation was used: 

 Yolo Bypass = Yolo Bypass + Putah + Sacramento + Willow 

 Inputs near Woodland Creek Weir Spill Slough 

To estimate total inflows to the Yolo Bypass on the days that average daily flows were less than 

1,000 cfs at Yolo Bypass near Woodland, the following equation was used: 

 Yolo Bypass = Cache Creek + Knights Landing + Fremont + Putah + Sacramento + Willow 

 Inputs @ Yolo Ridge Cut Weir Creek Weir Spill Slough 

Total outflow from the Yolo Bypass was estimated by subtracting 800 cfs from the total inflow to 

account flow trapped behind Lisbon Weir. If the estimated total inflow was less than 800 cfs, it 

was assumed that there was zero net flow past Lisbon Weir. As Figure E.3 illustrates, the 

average daily outflow estimates indicate that there is generally no net outflow between July and 

October, which is comparable with the preliminary outflow estimates described earlier that were 

developed by DWR and Regional Board staff using March-July 2004 flow data for the gage 

downstream of the Lisbon Weir. 

Concentration/Flow Regressions & Hydrologic Conditions in January 1995 
Delta Methylmercury TMDL Report E-8 April 2010 

Total mercury and TSS samples were collected from Prospect Slough near Toe Drain typically 

during outgoing tides. As described in Section 7.1.1.1, total mercury and TSS concentrations 

observed were regressed against estimated daily Yolo Bypass outflows at Lisbon Weir to 

determine if statistically significant correlations might exist (Appendix I, Figure I.1). There is 

generally no net outflow from the Yolo Bypass’s Toe Drain downstream of Lisbon Weir between 

July and October. Therefore, although sampling of Prospect Slough took place during outgoing 

tides with the intent of sampling outflows from the Yolo Bypass, during the summer months this 

sampling most likely represents waters tidally-pumped northward from Cache Slough, rather 

than outflows from the Yolo Bypass north of Lisbon Weir. 

Extremely high total mercury and TSS concentrations were measured in Prospect Slough on 

10 and 11 January 1995 (Figure I.1). Cache Creek Settling Basin (CCSB) and Fremont Weir 

spills were evaluated to determine whether these concentrations were likely to have occurred 

regularly during the 20-year study period. Flows from the CCSB are controlled by the following 

factors: (1) the CCSB can release up to 400 cfs through its low flow outlet; (2) above 400 cfs, 

the CCSB begins to fill at a rate of inflow (measured by the gage at Yolo) minus 400 cfs; and 

(3) when the basin fills beyond its capacity of approximately 43,200 acre-feet (weir height of 

12 feet multiplied by 3,600 acres, the area of the CCSB), water begins spilling over the weir. 

Weir spill continues until inflow to the CCSB decreases to 400 cfs (CDM, 2004). Cache Creek 

Settling Basin daily outflows were estimated based on these factors and compared to the timing 

of Fremont Weir spills (Figure E.4). The high concentrations observed in Prospect Slough on 

10 and 11 January 1995 may have resulted from the high releases from the Cache Creek 

Settling Basin that occurred on 9 January without any dilution flow from Fremont Weir. Although 

the CCSB has had such high releases several times throughout the 20-year record, all occurred 

concurrently with spills from Fremont Weir. Because the magnitude of CCSB release without 

any dilution that occurred on 9 January appears to have happened only once in the 20-year 

period, the 10 and 11 January 1995 total mercury and TSS concentration values were not 

included in the concentration/flow regressions used to predict average annual loads exported by 

the Yolo Bypass to the Delta. 

E.2.3 Precipitation-Based Water Volumes

Atmospheric wet deposition, tributary inputs from ungaged watersheds, and storm runoff from 

urban areas were estimated using the rational method: 

Qe = Rf x A x RC 

 Where: Qe = Estimated volumetric runoff rate (acre-feet per year) 

 Rf = Annual precipitation amount in the watershed (feet per year) 

 A = Watershed area (acres) 

 RC = Runoff coefficient 

Precipitation data for seventeen gages located throughout the Delta source region (Table E.3) 

were compiled with a focus on gages that appeared to represent the general precipitation 

pattern of each region and had records at least 20 years in length. All but one of the gages 

used in this analysis had records that exceeded 20 years in length. The average annual 
Delta Methylmercury TMDL Report E-9 April 2010 

precipitation amount for WY2000-2003 and WY1984-2003 were calculated for each gage. Land 

use information was obtained from the California Department of Water Resources Land Use 

Survey Data and USGS/USEPA National Land Cover Data (DWR, 1993-20026

, USGS/USEPA, 

19937

) to determine acreages for each land use in the Delta and its ungaged tributary 

watersheds. The Delta and its ungaged tributary subwatersheds were divided into areas 

defined by (1) proximity to a precipitation gage, and (2) land use category. Because of their 

size, tables of the land use acreages divided by land use type and precipitation area are not 

included in this appendix but can be provided electronically upon request. Table E.4 provides 

just the urban acreage in the Delta. Then runoff coefficients were assigned to each land use 

type (Table E.5). Using a combination of software programs (Microsoft Excel and ESRI 

ArcView), 4-year and 20-year average annual stormwater runoff amounts were calculated for 

each subarea using Equation E.1. 

Dry weather urban runoff was estimated by adapting the daily dry season runoff values 

developed by Larry Walker Associates (LWA, 1996) for the Sacramento region. Larry Walker 

Associates determined average dry season runoff to be 49 mgd and inter-storm runoff to be 

58 mgd in the greater Sacramento region. LWA estimated that there were 302 square miles 

(193,280 acres) of urban area in the Sacramento region. The daily dry season runoff value was 

divided by the acreage to obtain dry season runoff volume per acre: 

 Dry Season Runoff = 49 x 106

 gallons/day ÷ 193,280 acres 

 = 254 gallons/acre/day 

It was assumed that the dry season runoff amounts in the greater Sacramento region are 

representative of all urban areas within the statutory Delta boundary and its ungaged tributary 

watersheds. LWA's dry season runoff estimates were used for dry days in both the dry season 

and wet season to estimate the annual average non-storm urban runoff in the Delta. The 

average number of non-rain days per year for the WY1984-2003 period (305 days) was 

multiplied by 254 gallons/acre/day and the Delta urban acreage (about 55,000 acres), to obtain 

an average annual runoff volume of 4,300 million gallons per year (13,000 acre-feet/year). 

E.2.4 Dayflow Model 

Output from the Dayflow Model was used to estimate the average annual water volume of 

outflows to San Francisco Bay and diversions south of the Delta via the Delta Mendota Canal 

(Central Valley Project pumping at Tracy) and State Water Project (Clifton Court Intake). 

Dayflow is a computer program maintained by the California Department of Water Resources 

Interagency Ecological Program (http://www.iep.ca.gov/dayflow/index.html). It was developed in 

1978 as an accounting tool for determining historical Delta boundary hydrology (mean daily 

flows). In 2000, the software used to perform Dayflow calculations was rewritten in Java. The 

input data include the principal Delta stream inflows, Delta precipitation, Delta exports, and 

Delta gross channel depletions. These data include both monitored and estimated values. 

 

6

 DWR. 1993-2003. Land Use Data. California Department of Water Resources. Available at: 

http://www.landwateruse.water.ca.gov/basicdata/landuse/digitalsurveys.cfm. 7

 USEPA/USGS Multi-Resolution Land Characterization Program National Land Cover Data available at: 

http://www.epa.gov/mrlc/nlcd.html. 
Delta Methylmercury TMDL Report E-10 April 2010 

Input data is stored in a HEC-DSS file, and output is written to an ASCII file. Dayflow output is 

used extensively in studies initiated by the Department of Water Resources, the Department of 

Fish and Game, and by other State and Federal agencies and private consultants. Dayflow 

output files can be downloaded from the IEP Dayflow website: 

http://www.iep.ca.gov/dayflow/output/index.html. 

E.2.6 Evaporation

The amount of water lost through evaporation from Delta water surfaces was estimated by 

multiplying the average evaporation rate for the region by the water surface acreage. Mean 

evaporation at Brannan Island and Grizzly Island near Rio Vista is approximately 73.4 inches 

per year. Mean evaporation at the Oakdale Woodward Dam Station south of Stockton is 

approximately 78.43 inches per year. Staff used an evaporation rate of 73.4 inches per year 

and a water surface acreage of approximately 48,600 acres (1.97 x 108

 square meters) (see 

Section 4.4.3) to estimate an evaporation water loss of about 300,000 acre/feet per year. 

E.2.7 Dredging

Sediment is dredged at various locations in the Delta to maintain ship channels and marinas. 

Table 6.17 in Chapter 6 provides details on recent dredge projects within the Delta and 

Figure 6.9 shows their approximate locations. Approximately 533,400 cubic yards per year 

(cy/yr) of sediment are dredged on average. The amount of water removed by dredge projects 

was estimated using weight-volume relationships for saturated soils described by Das (1990)8

, 

specific gravity values of 1 and 2.65 for water and solids, respectively, and the assumption that 

the water content of the dredged material is 100% (50% water and 50% sediment by weight9

): 

 Water Volume = 

= (dredged material [cy/yr]) x (1 + (1 ÷ 2.65)) x (cy to acre-feet conversion factors) 

= 533,400 cy x (1 ÷ 1.3774) x (27 ÷ 43,560) 

= 240 acre-feet/yr 

This estimate does not account for how much water is removed by dredging activities that 

incorporate river water with the dredge sediment to form a slurry that can then be pumped and 

delivered via pipeline to dredge material disposal sites for settling and disposal. Nor does the 

estimate account for return water discharged by disposal sites to adjacent receiving waters. 

 

8

 Das, B.M. 1990. Principles of Geotechnical Engineering. Second Edition. PWS-Kent Publishing Company, Boston, 

665 pp. 9

 This is a common assumption for dredging operations. (U.S. Army Corps of Engineers. 2002. “Moisture Content,” 

personal communication from L. Fade to G. Collins, San Francisco Bay Regional Water Quality Control Board, 

October.) 
Delta Methylmercury TMDL Report E-11 April 2010 

Figure E.1: California Dept. Water Resources Chronological Reconstructed Sacramento Valley 

& San Joaquin Valley Water Year Hydrologic Classification Indices (DWR, 2005)

SACRAMENTO VALLEY

2

4

6

8

10

12

14

16

1900 1920 1940 1960 1980 2000

Water Year

Water Index

WY2000

to 2003

WY1984 to 2003

Wet

Dry

Normal

Critical

Dry

SAN JOAQUIN VALLEY

0

2

4

6

8

1900 1920 1940 1960 1980 2000

Water Year

Water Index

WY2000

to 2003

WY1984 to 2003

Wet

Dry

Normal

Critical

Dry
Delta Methylmercury TMDL Report E-12 April 2010 

Figure E.2: Hydrologic Features of the Yolo Bypass.
Delta Methylmercury TMDL Report E-13 April 2010 

Figure E.3: Estimated Average Daily Outflows from the Yolo Bypass below Lisbon Weir during 

[A] WY2000-2003 and [B] WY1984-2003 

0

100,000

200,000

300,000

400,000

500,000

Oct-83 Oct-85 Oct-87 Oct-89 Oct-91 Oct-93 Oct-95 Oct-97 Oct-99 Oct-01

Average Daily Flow (cfs)

B. W Y1984-2003

0

20,000

40,000

60,000

Oct99Apr00Oct00Apr01Oct01Apr02Oct02Apr03Oct03

Average Daily Flow (cfs)

A. W Y2000-2003
Delta Methylmercury TMDL Report E-14 

Figure E.4: Comparison of Estimated Cache Creek Settling Basin (CCSB) Outflows Compared to Fremo

January 9, 1995

0

5,000

10,00015,00020,00025,00030,00035,00040,000

Oct-83 Oct-84 Oct-85 Oct-86 Oct-87 Oct-88 Oct-89 Oct-90 Oct-91 Oct-92 Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-9

Flow (cfs)

CCSB Weir SpillsCCSB Weir Spills When Fremont Weir Is Not SpillingCCSB Weir Spills When Fremont Weir Is Not Spilling and/or Before FW SpillsFremont Weir SpilledSacramento Weir Spilled
Delta Methylmercury TMDL Report E-15 April 2010 

 Table E.1: Methods Used to Estimate Average Annual Water Volumes for Delta and Sacramento Basin 

Inputs and Exports 

Type Method Location of Method Description 

Tributary Inputs 

American River @ Discovery Park 

Cache Creek Settling Basin 

Colusa Basin Drain 

Feather River nr Nicolaus 

Fremont Weir 

Marsh Creek 

Mokelumne River d/s I-5 

Sacramento River above Colusa 

Sacramento River @ Freeport 

San Joaquin River @ Vernalis 

Sutter Bypass 

Flow -Gage Based Method Section E.2.1 

Yolo Bypass Outflows 

Knights Landing Ridge Cut 

Putah Creek @ Mace Blvd. 

Willow Slough 

Flow-Gage + Hydrologic Model Section E.2.2 

Bear/Mosher Creek 

Calaveras River/Mormon Slough 

Coon Creek/Cross Canal 

French Camp Slough / Lone 

Tree Creek 

Morrison Creek 

Natomas East Main Drain 

Ulatis Creek 

Other Small Drainages to the Delta 

Precipitation-Based Method Section E.2.3 

Other Inputs 

Wastewater Discharges Project Files Tables G.1 and G.2 (Appendix G) 

Atmospheric deposition Precipitation-Based Method Section E.2.3 

Urban runoff Precipitation-Based Method 

+ Dry Weather Estimate Section E.2.3 

Exports 

Delta Mendota Canal 

State Water Project 

Outflows to San Francisco Bay 

Dayflow Model Section E.2.4 

Agricultural Diversion Delta Island Consumptive Use Model Section 6.2.4 (Chapter 6) 

Evaporation Evaporation Rate x Water Acreage Section E.2.5 

Dredging Project Files Section E.2.6 
Delta Methylmercury TMDL Report E-16 April 2010 

Table E.2: Gage Records Used to Calculate Average Annual Water Volumes for Delta and Sacramento Basin 

Tributaries. 

Gage Name Gage Operator Gage ID (a) Period of Record Data Type 

American River @ Fair Oaks USGS and DWR 11446500 10/1/1904 - present Daily 

Bear River near Wheatland USGS and DWR BRW 1/24/97 - present Event 

Butte Slough near Meridian 

(Sutter Bypass) DWR BSL 10/1/1975 - present Daily 

Cache Creek @ Yolo USGS and DWR 11452500 4/1/1903 - present Daily 

Colusa Basin Drain near Hwy 20 DWR CDR, A02976 

3/12/97 - present (CDR), 

5/1/41 - present 

(A02976) 

Event (CDR), 

Daily (A02976)

Colusa Basin Drain @ Knights 

Landing DWR A02945 10/1/1975 - present Daily 

Feather River @ Gridley DWR GRL 1/1/93 - present Daily 

Feather River near Nicolaus USGS 11425000 4/1/42 - 9/30/83 Daily 

Fremont Weir DWR FRE 10/1/1983 - present Daily 

Cosumnes River @ Michigan Bar USGS and DWR MHB 1/1/93 - present Daily 

Marsh Creek @ Brentwood USGS 11337600 8/26/2000 - present Daily 

Mokelumne River @ Woodbridge East Bay Municipal 

Utility District & USGS WBR, 11325500 6/1/24 - 9/30/01 Daily 

Putah Creek Outflow at Putah 

Diversion Dam USBR 1/1/98 - present Daily 

Lake Solano Calculated Inflow USBR 1/1/98 - present Daily 

Lake Berryessa Outflow USBR BER 10/4/93 - present Daily 

Sacramento River @ Colusa USGS & DWR COL 1/1/92 -present Daily 

Sacramento River @ Freeport USGS FPT 10/1/48 - present Daily 

San Joaquin near Vernalis USGS & DWR 11303500, VNS 

10/1/23 - present 

(11303500), 1/1/93 - 

present 

Daily 

Yolo Bypass near Woodland USGS & DWR 11453000, YBY 

6/29/98 - 7/13/98 (YBY), 

10/1/39 - 3/17/03 

(11453000) 

Daily 

Yuba River near Marysville USGS 11421000 10/1/43 - present Daily 

(a) Letter-based “Gage ID” records were accessed through the California Data Exchange Center (CDEC) website, 

http://cdec.water.ca.gov. Alphanumeric “Gage ID” records were accessed through the DWR’s Water Data Library website, 

http://wdl.water.ca.gov/hydstra/index.cfm. Numeric “Gage ID” records were accessed through the U.S. Geological Survey SurfaceWater Data for the Nation website, http://waterdata.usgs.gov/nwis/sw. Putah Creek outflow at the Putah Diversion Dam and Lake

Solano Calculated Inflow were accessed through the U.S. Bureau of Reclamation Reservoir Operations Reports website, 

http://www.usbr.gov/mp/cvo/reports.html. 
Delta Methylmercury TMDL Report E-17 April 2010 

Table E.3: Summary of Precipitation Data Used to Estimate Runoff 

Station (a) Code Latitude Longitude 

Beginning of 

Record (b)

Data 

Type 

WY2000-

2003 

Average 

WY1984-

2003 

Average 

Adin RS ADN 41.194 -120.944 10/01/1943 MA (c) 11.5 15.1 

Calaveras Big Trees CVT 38.283 -120.317 10/01/1929 MA 48.6 53.1 

Capay CPY 38.730 -122.130 01/01/1905 MA 20.4 22.5 

Englebright (USACE) ENG 39.239 -121.267 03/01/1989 MA 33.0 34.5 

Fiddletown FDD 38.533 -120.700 12/01/1937 MA 33.2 35.5 

Folsom Dam FLD 38.700 -121.167 10/01/1955 MA 22.2 24.2 

Foresthill R S FRH 39.017 -120.850 10/01/1936 MA 46.1 50.4 

Los Banos LSB 37.050 -120.867 01/01/1905 MA 7.8 9.5 

New Exchequer-Lk McClure EXC 37.585 -120.270 10/01/1935 MA 18.8 19.4 

North Fork R S NFR 37.233 -119.500 01/01/1905 MA 30.1 33.0 

Orland ORL 39.750 -122.200 01/01/1905 MA 18.7 21.6 

Quincy RS (USFS) QNC 39.960 -120.950 01/01/1905 MA 36.9 36.4 

Sacramento WB City SCR 38.583 -121.500 01/01/1905 MA 18.7 19.5 

Shasta Dam (USBR) SHA 40.718 -122.420 10/01/1957 DA (c) 63.6 61.4 

Stockton Fire Station 4 STK 38.001 -121.317 01/01/1905 MA 16.6 17.2 

Stony Gorge Reservoir STG 39.583 -122.533 10/01/1926 MA 20.2 20.9 

Yosemite Headquarters YSV 37.740 -119.583 01/01/1905 MA 32.3 36.3 

(a) All precipitation records were obtained from CDEC, http://cdec.water.ca.gov. 

(b) All records continue through WY2003. 

(c) MA: monthly accumulated; DA: daily accumulated. 

Table E.4: Urban Acreage within the Legal Delta Boundary and Yolo Bypass North of the Delta 

Precipitation Gage Region / Land Use Code (a)

Delta Subarea Los Banos Sacramento WB City Stockton Fire Station 4 (a)

U UI UR T T U UC UI UR UT T U UI UR UT

Grand 

Total 

Central Delta 11 50 121 30 42 1276 12955 983 317 15,785 

Marsh Creek 67 2891 88 381 3,427 

Mokelumne River 26 57 44 39 166 

Sacramento River 728 6286 225 206 921 198 258 176 107 38 9,143 

San Joaquin River 9 1 0.3 21 2372 6802 2232 2125 13,562 

West Delta 3 21 11 2 27 136 446 8423 323 335 23 9,750 

Yolo Bypass-North 505 1407 40 1080 48 32 3,112 

Yolo Bypass-South 437 168 7 3 43 658 

(a) Acreages rounded after water volume and load calculations were made. Land use codes are defined in Table E.5. 

Acreages by subarea obtained using DWR land use GIS coverages (1993-2003) and ArcGIS [GIS software], Version 9.2, 

Redlands, CA: Environmental Systems Research Institute, Inc., 1999-2006. As described in Section 6.2.5, urban acreages 

corresponding to each MS4 permittee within each subarea were determined using available MS4 service area delineations 

(e.g., paper and electronic maps provided by the MS4 Permittees and 1990 city and county boundaries). Because of their 

size, these more detailed delineations are not included in this appendix but are available upon request. 
Delta Methylmercury TMDL Report E-18 April 2010 

Table E.5: Land Uses and Runoff Coefficients 

Code Definition (a) Runoff Coefficient 

Agriculture - Other, mixed, or uncategorized 0.175 

Barren 0.300 

Commercial [UC] 0.71 

Crop & Pasture - uncategorized 0.175 

Entry Denied 0.175 

Industrial [UI] 0.70 

Landscaped (irrigated lawns, cemeteries, parks) 0.22 

Native Vegetation - uncategorized 0.150 

Open Recreation 0.175 

Orchard 0.200 

Orchard & Vineyard - uncategorized 0.200 

Pasture 0.175 

Rangeland 0.150 

Residential [UR] 0.50 

Rice Fields 0.175 

Row and Field Crops 0.175 

Strip Mine or Quarry 0.3 

Transitional [UT] 0.70 

Transportation, Communication, Utilities [T] 0.700 

Urban unclassified (includes mixed use) [U] 0.56 

Vineyard 0.200 

Water 1.000 

Wetland and Marsh 0.150 

(a) Staff adapted runoff coefficients provided by: Lindeburg, M.R. 1992. Civil 

Engineering Reference Manual. Sixth Edition. Professional Publications, 

Inc.: Belmont, CA. Appendix A: Rational Method Runoff Coefficients. Urban 

land use codes used in Table E.4 are noted in brackets. 
Delta Methylmercury TMDL Report F-1 April 2010 

F. SUMMARY OF METHYLMERCURY CONCENTRATION DATA FOR MAJOR DELTA 

TRIBUTARY INPUT AND EXPORT LOADS 

The monthly average methylmercury concentrations and water volumes used to estimate the 

WY2000-2003 annual average methylmercury loads for tributary inputs and exports are 

presented in Tables F.1 and F.2, respectively. Methylmercury concentration data for these and 

other major Sacramento Basin tributaries are included in Appendix L. Figures F.1a, F.1b, 

and F.2 present the plots of methylmercury concentration versus daily flow for each tributary 

input and export monitoring station with daily flow data available.
Delta Methylmercury TMDL Report F-2 

Table F.1: Monthly Average Methylmercury Concentrations (ng/l) for March 2000 to April 2004 Period Used to Estimate An

Month 

Cache 

Creek 

Settling 

Basin 

Outflow (b)

Delta 

Mendota 

Canal 

Feather 

River 

near 

Nicolaus

Fremont Weir 

(Sacramento 

River @ 

Colusa) (c)

Knights 

Landing Ridge 

Cut (Colusa 

Basin Drain @ 

Road 99E) 

Mokelumne 

River @ I-5 

Outflow to 

San Francisco 

Bay (X2) 

Putah 

Creek @ 

Mace Blvd

Sacramen

River @ 

Freepor

January 0.144 0.079 0.067 0.434 0.246 0.095 0.078 0.145 

February 0.328 0.133* 0.104 0.100 0.181 0.320 0.165 0.29 0.146 

March 0.324 0.123 0.118 0.186 0.251 0.178 0.204 0.168 0.093 

April 0.155 0.018 0.109 0.069* 0.096 0.247 0.061 0.12 0.066 

May 0.532 0.094 0.172 0.103 0.086 0.174 0.119 0.456 0.111 

June 0.421 0.071 0.106 0.155* 0.090 0.161 0.077 0.193 0.084 

July 0.960 0.056 0.035 0.048* 0.088 0.066 0.050 0.189 0.105 

August 0.021 0.052* 0.071* 0.086* 0.110 0.033 0.181 0.093 

September 0.991 0.035 0.069 0.094* 0.084 0.099 0.043 0.139 0.071 

October 0.011 0.088 0.124* 0.183 0.130 0.011 0.114 0.077 

November 0.037* 0.113 0.097* 0.421 0.113* 0.035* 0.083* 0.123 December 0.063 0.096* 0.054 0.428* 0.096 0.060 0.053 0.122 

Average of 

All Data 0.504 0.062 0.103 0.105 0.214 0.153 0.075 0.197 0.105 

Median of 

All Data 0.432 0.061 0.096 0.089 0.125 0.167 0.070 0.126 0.097 

Annual 

Average (d) 0.504 0.064 0.099 0.102 0.191 0.166 0.083 0.180 0.103 

(a) No methylmercury concentration data were available for the month of February at the Delta Mendota Canal monitoring station, the months of August 

Feather River and Colusa Basin Drain monitoring stations, or for the month of November at the Delta Mendota Canal, Mokelumne River, Putah Cree

Water Project, and X2 monitoring stations. Monthly average methylmercury concentrations were estimated for the months with no data by averaging months before and after the month with no data; these estimated values are shown in bold, italicized text with an asterisk. 

(b) Sampling at the Cache Creek Settling Basin Outflow did not take place monthly; therefore all available methylmercury concentration data were avera

average methylmercury concentration. 

(c) Fremont Weir did not spill during months that are highlighted in gray and noted with an asterisk. The annual average methylmercury concentration f

estimated by averaging the monthly averages of the months when a spill occurred. 

(d) The annual average concentration was estimated by averaging the monthly averages (not including months during which no samples were collected

Settling Basin and Fremont Weir. The methods used for these two locations are described in footnotes (b) and (c), respectively.
Delta Methylmercury TMDL Report F-3 

Table F.2: Monthly Average Water Volumes (acre-ft/month) for WY2000-2003 Used to Estimate Annual Average Loads. 

Month 

Cache 

Creek 

Settling 

Basin 

Outflow 

Delta 

Mendota 

Canal 

Fremont 

Weir 

Knights 

Landing 

Ridge Cut 

Inflow to 

Yolo Bypass 

Mokelumne 

River @ I-5 

Outflow to 

San Francisco 

Bay (X2) 

Putah 

Creek @ 

Mace Blvd

Sacramento 

River @ 

Freeport 

January 61,650 220,976 110,745 86,228 42,065 1,954,767 489 2,028,832 

February 28,463 217,720 467,038 40,250 83,824 2,207,169 5,041 1,943,680 

March 46,893 212,535 479,532 33,301 81,111 2,217,055 15,743 1,963,652 

April 23,334 125,614 0 6,518 53,898 1,092,635 4,594 1,117,939 

May 14,559 68,390 56 11,575 51,465 1,340,314 7,837 1,278,515 

June 1,621 193,597 0 2,344 30,773 526,409 774 963,395 

July 989 261,949 0 5,041 17,305 447,565 799 1,187,600 

August 957 264,294 0 3,901 9,269 305,230 268 1,039,802 

September 704 251,515 0 179 5,873 242,934 11 841,082 

October 2,224 249,026 0 5,804 10,175 283,774 0 651,856 

November 1,782 233,733 0 10,852 18,901 403,620 460 747,823 December 38,739 207,372 3,081 46,981 25,680 1,079,304 5,360 1,335,662 

Average Annual 

Water Volume 

(M Acre-ft/yr) 

0.22 2.5 1.1 0.25 0.43 12.1 0.041 15.1 
Delta Methylmercury TMDL Report F-4 April 2010 

Figure F.1a: Methylmercury Concentration versus Daily Flow for Tributary Inputs 

with Daily Flow Data Available. 

San Joaquin River @ Vernalis

y = -0.022Ln(x) + 0.3271

R2 = 0.059

0

0.1

0.2

0.3

0 2,000 4,000 6,000 8,000

Flow (cfs)

MMHg Conc. (ng/l)

Sacramento River @ RM44

y = 0.0363Ln(x) - 0.2354

R2 = 0.169

0

0.1

0.2

0.3

0 20,000 40,000 60,000 80,000

Flow (cfs)

MMHg Conc. (ng/l)

Mokelumne River near I-5

y = 0.0193Ln(x) + 0.0236

R2 = 0.0165

0

0.1

0.2

0.3

0 1,000 2,000 3,000

Flow (cfs)

MMHg Conc. (ng/l)

Sacramento River @ Greene's Landing

y = 2E-06x + 0.0727

R2 = 0.1245

0

0.1

0.2

0.3

0 20,000 40,000 60,000 80,000

Flow (cfs)

MMHg Conc. (ng/l)

Sacramento River @ Freeport

y = 0.0354Ln(x) - 0.2398

R2 = 0.1459

0

0.1

0.2

0.3

0 20,000 40,000 60,000 80,000

Flow (cfs)

MMHg Conc. (ng/l)

Marsh Creek

y = 0.1967e0.0056x

R2 = 0.0414

0

0.1

0.2

0.3

0 20 40 60

Flow (cfs)

MMHg Conc. (ng/l)
Delta Methylmercury TMDL Report F-5 April 2010 

Figure F.1b: Methylmercury Concentration versus Daily Flow for Tributary Inputs 

with Daily Flow Data Available. 

Cache Creek Settling Basin Outflow

y = -0.0795Ln(x) + 0.8893

R2 = 0.5721

0

0.4

0.8

1.2

0 2,000 4,000 6,000

Flow (cfs)

MMHg Conc. (ng/l)

Knights Landing Ridge Cut (Colusa Basin 

Drain @ Road 99E)

y = 0.1343e0.0006x

R2 = 0.2211

0

0.2

0.4

0.6

0 1,000 2,000 3,000

Flow (cfs)

MMHg Conc. (ng/l)

Feather River near Nicolaus

y = 2E-09x2 - 3E-05x + 0.1673

R2 = 0.0929

0

0.1

0.2

0.3

0 2,500 5,000 7,500 10,000

Flow (cfs)

MMHg Conc. (ng/l)

Putah Creek @ Mace Blvd

y = 0.1583e-0.0007x

R2 = 0.0195

0

0.4

0.8

1.2

0 100 200 300 400 500

Flow (cfs)

MMHg Conc. (ng/l)

Fremont Weir 

(Sacramento River @ Colusa)

y = 4E-10x2 - 1E-05x + 0.1582

R2 = 0.4856

0

0.1

0.2

0.3

0 10,000 20,000 30,000 40,000

Flow (cfs)

MMHg Conc. (ng/l)
Delta Methylmercury TMDL Report F-6 April 2010 

Figures F.2: Methylmercury Concentration versus Daily Flow for Exports 

with Daily Flow Data Available. 

Delta Outflow s to SFBay (X2)

y = 2E-06x + 0.0433

R2 = 0.2121

0

0.1

0.2

0.3

0 20,000 40,000 60,000

Flow (cfs)

MMHg Conc. (ng/l)

State Water Project

y = 0.1488x-0.1571

R2 = 0.0112

0

0.1

0.2

0.3

0 5,000 10,000

Flow (cfs)

MMHg Conc. (ng/l)

Delta Mendota Canal

y = 0.0625e-0.0001x

R2 = 0.0267

0

0.1

0.2

0.3

0 2,000 4,000 6,000

Flow (cfs)

MMHg Conc. (ng/l)
Delta Methylmercury TMDL Report G-1 

G. INFORMATION ABOUT NPDES-PERMITTED FACILITIES IN THE DELTA AND ITS TRIBUTARY W

Table G.1: Summary of Unfiltered Total Mercury Concentrations in Discharges from Facilities within the Delta and Yolo By

Facility Name (NPDES #) (a) Facility Type 

Delta 

Subarea 

Average

Daily 

Discharge

(mgd)

TotHg 

Sampling

Period 

Ave.

Conc. 

(ng/l)

Conc.

Range

(ng/l)

# of 

Samples

Standard 

Deviation

t Va

(p = 0

conf 9

df = 

Brentwood WWTP (CA0082660) Mun. WWTP Marsh Ck 3.1 8/04-10/05 1.3 0.6- 2.2 15 0.54 2.1

Davis WWTP (CA0079049) 

Discharge 001 (e) Mun. WWTP Yolo Bypass 2.8 8/04-1/05, 7/05 7.4 2.0-10.8 7 2.84 2.4

Davis WWTP (CA0079049) 

Discharge 002 (e) Mun. WWTP Yolo Bypass 2.4 2/05-6/05 6.9 4.8-10.5 5 2.43 2.7

Deuel Voc.Inst. WWTP (CA0078093) Mun. WWTP San Joaquin 0.47 3/02-12/02 3.3 2.5-4.6 4 0.90 3.1

Discovery Bay WWTP (CA0078590) Mun. WWTP Central 1.5 8/04-10/05 5.0 1.8- 11.0 10 2.76 2.2

GWF Power Systems (CA0082309) Power West 0.05 4/01-10/05 4.3 0.6- 25.7 42 3.74 2.0

Lincoln Center Groundwater 

Treatment Facility

Groundwater 

Treatment Central 0.25 11/05-06/07 0.57 <0.2-1.6 20 0.38 2.0

Lodi White Slough WWTP 

(CA0079243) Mun. WWTP Central 4.5 8/04-10/05 3.3 1.6-7.2 15 1.38 2.1

Manteca WWTP (CA0081558) Mun. WWTP San Joaquin 4.63 9/04-10/05 10.7 2.0-20.3 14 5.91 2.

2.90 2/04-5/05 6.1 1.6-10.1 4 4.14 3.1

Mirant Delta LLC Contra Costa 

Power Plant, Outfall 1 & 2 

(CA0004863) 

Power West 

121.03 2/04-5/05 7.1 4.1-11.8 4 3.64 3.1

Oakwood Lake Subdivision Mining 

Reclamation (CA0082783) (c) Lake Dewatering San Joaquin 9.15 1/02-11/02 2.9 2.1-3.9 4 0.97 3.1

Rio Vista Trilogy WWTP 

(CA0083771) (d) Mun. WWTP Sacramento 0.10 1/03 3.7 3.7 1 -- -

Rio Vista WWTP (CA0079588) Mun. WWTP Sacramento 0.47 12/01-12/03 9.5 1.7-19 20 4.69 2.0

San Joaquin Co DPW CSA 31 

Flag City WWTP (CA0082848) Mun. WWTP Central 0.06 1/05-10/05 3.2 0.6-17 8 5.57 2.3

SRCSD Sacramento River WWTP 

(CA0077682) Mun. WWTP Sacramento 162 10/99-9/03 7.59 2.9-16.2 195 2.23 1.9

SRCSD Walnut Grove WWTP 

(CA0078794) Mun. WWTP Sacramento 0.08 12/00-1/04 21.5 11-29.4 9 5.24 2.3

State of California Central 

Heating/Cooling Plant (CA0078581) Heating /Cooling Sacramento 5.26 3/02-12/02 2.8 1.1-3.7 4 1.19 3.1

Stockton WWTP (CA0079138) Mun. WWTP San Joaquin 28 8/04-7/05 5.2 3.0-11 12 3.00 2.2

Tracy WWTP (CA0079154) Mun. WWTP San Joaquin 9.49 8/04-8/05 11.0 2.1-18.6 13 4.43 2.1

West Sacramento WWTP 

(CA0079171) Mun. WWTP Sacramento 5.60 8/04-7/05 3.3 1.6-5 11 1.08 2.2

Woodland WWTP (CA0077950) Mun. WWTP Yolo Bypass 6.05 8/04-7/05 6.1 0.91-53 12 1.08 2.2
Delta Methylmercury TMDL Report G-2 April 2010 

Table G.1 Footnotes:

(a) The sum of annual facility effluent total mercury discharge loads is 2,284 g/yr. No mercury data are yet available for 

Metropolitan Stevedore (CA0084174), a marine bulk commodity terminal in the Central Delta subarea. Mercury and flow data 

for the Sacramento Combined WWTP (CA0079111) in the Sacramento River subarea are summarized in Table G.2. If the 

estimated loading from the Combined WWTP is included (151 g/yr, see Table G.2b), the total mercury loading to the Delta 

from NPDES facilities is approximately 2,435 g/yr or 2.4 kg/yr. 

(b) Based on the comparison of the available intake and outfall mercury data for the Mirant Delta facility and other similar facilities 

that discharged to the Delta in years past (Table G.5 in Appendix G), such facilities may not act as measurable sources of 

mercury to the Delta. According to its NPDES permit, the Central Heating/Cooling Plant adds no chemicals to its supply water; 

however, the permits for Mirant Delta and other similar facilities in the tributary watersheds indicate that mercury-containing

chemicals may be added to their cooling water and other low-volume waste streams may be included in their discharges (see 

Tables G.6 and G.7). Staff recommends that the assumption that power and heating/cooling plants do not contribute mercury 

to Delta and upstream surface waters be re-evaluated as additional information becomes available. 

(c) The Oakwood Lake Subdivision Mining Reclamation was formerly known as the Manteca Aggregate Sand Plant. 

(d) The City of Rio Vista’s Trilogy WWTP was replaced by the Northwest WWTP, which began discharging to the Sacramento 

River subarea in 2007 under the same NPDES permit (CA0083771). The Northwest WWTP has a startup dry weather 

discharge of 1 mgd and peak discharge of 3 mgd. No effluent methylmercury concentration data were available for either the 

Trilogy or Northwest WWTPs, and no effluent total mercury concentration data were available for the Northwest WWTP, at the 

time the Delta methylmercury TMDL was developed. The above total mercury load is based on effluent total mercury 

concentration data available for the Trilogy WWTP and may not be characteristic of Northwest WWTP discharges. The 

Northwest WWTP effluent total mercury loads will be determined once it completes one year of monthly monitoring of its 

discharge. 

(e) The City of Davis WWTP (CA0079049) has two seasonal discharge locations; wastewater is discharged from Discharge 001 to 

the Willow Slough Bypass upstream of the Yolo Bypass and from Discharge 002 to the Conaway Ranch Toe Drain in the Yolo 

Bypass. The Discharge 001 total mercury load is based on effluent volumes for October 2004 through January 2005 plus July 

2005 through September 2005. The Discharge 002 total mercury load is based on effluent volumes for February 2005 through 

June 2005. Because the discharge to Willow Slough is outside of the Delta/Yolo Bypass, it is not included in the sum of facility 

loads.
Delta Methylmercury TMDL Report G-3 April 2010 

Table G.2a: Summary of City of Sacramento Combined Sewer System Total Mercury Concentration 

Data (a, b)

DATE CWTP (ng/l) SUMP-2 (ng/l) PIONEER (ng/l)

12/03/1994 58 82 32 

01/08/1995 47 120 

01/10/1995 220 

03/02/1995 90 98 

03/09/1995 85 

03/21/1995 68 83 

Average 66 101 104 

# of Samples 4 2 5 

Standard Deviation 18.30 26.87 69.78 

t value 

(p=0.975, conf 95%, df =n-1) 3.182 12.706 2.776 

Confidence Interval 29 241 87 

(a) The City of Sacramento owns and operates a combined sewer system (CSS) that serves 7,510 acres in the downtown, East 

Sacramento, and Land Park areas. An additional 3,690 acres with separate sewers contributes sanitary sewage to the 

combined system. The CSS conveys domestic and industrial wastewater and storm runoff to Sump 2, where up to 60 mgd is 

pumped to the Sacramento Regional County Sanitation District's regional wastewater treatment plant (SRCSD) for secondary 

treatment prior to discharge to the Sacramento River. This discharge is designated as point 001 and is governed by NPDES 

No. CA0077682. When flow to Sump 2 exceeds 60 mgd, the City operates its Combined Wastewater Treatment Plant (CWTP), 

where an additional 130 mgd of combined wastewater receives primary treatment with disinfection and discharge to the 

Sacramento River at points 002 and 003. The CWTP basins may also be used for storage of flows and diversion of flows back 

to the SRCSD. Flows to Sump 2 greater than 190 mgd are diverted to the 28 million gallon Pioneer Interceptor and Reservoir 

for storage. During major storms, Sump 1/1A also pumps up to 120 mgd to Pioneer Reservoir. The stored combined 

wastewater is diverted back to the SRCSD or the CWTP for treatment as treatment capacity allows, or is discharged to the 

Sacramento River if storm flows exceed total treatment and storage capacity. The discharge from Pioneer Reservoir occurs at 

point 006 and receives partial settleable solids and floatables removal, in a flow-through process, without disinfection. During 

extreme high flow conditions, discharges of untreated combined wastewater may occur at Sump 2 bypass points 004 and 005 

and at Sump 1 bypass point 007. Collected screenings are hauled to a landfill, and sludges and other solids removed from 

liquid wastes are pumped through the collection system to the SRCSD. 

(b) Total mercury concentration data were obtained from a City of Sacramento monitoring report to the Regional Board (City of 

Sacramento, 1996). Only data collected using clean hands techniques (MDL of 0.1 ng/l) were used for TMDL calculations. 

 

 Table G.2b: City of Sacramento Combined Stormwater/Sewer System Annual Water Volumes & 

Total Mercury Load Estimates 

Water Volume(a) (MG/year) Total Mercury Load (b) Water (kg/year)

Year CWTP PIONEER SUMP 2 TOTAL CWTP PIONEER SUMP 2 TOTAL 

1993 459.6 42.5 243.9 746.0 0.114 ±0.051 0.017 ±0.038 0.093 ±0.082 0.224 ±0.171

1994 190.5 18.6 209.0 0.047 ±0.021 0.007 ±0.006 0.054 ±0.027

1995 399.7 189.7 435.9 1025.3 0.099 ±0.044 0.074 ±0.171 0.167 ±0.147 0.341 ±0.363

1996 433.7 259.8 89.3 782.8 0.108 ±0.048 0.102 ±0.235 0.034 ±0.030 0.244 ±0.313

1997 354.3 139.0 210.9 704.2 0.088 ±0.039 0.055 ±0.126 0.081 ±0.071 0.223 ±0.236

1998 440.2 515.1 955.3 0.110 ±0.049 0.202 ±0.46 0.312 ±0.514

1999 8.3 65.4 73.7 0.002 ±0.001 0.026 ±0.059 0.028 ±0.060

2000 90.8 291.3 82.9 465.0 0.023 ±0.01 0.114 ±0.263 0.032 ±0.028 0.169 ±0.301

2001 32.6 32.6 0.013 ±0.029 0.013 ±0.029

2002 53.7 53.7 0.021 ±0.049 0.021 ±0.049

2003 90.6 90.6 0.036 ±0.082 0.036 ±0.082

Average Annual Water Volume (MG/year): 467 Average Annual TotHg Load (kg/year): 0.151 ±0.195

(a) Annual water volumes discharged to the Sacramento River obtained from City of Sacramento annual monitoring reports. 

(b) Total mercury load estimates are based on average total mercury concentrations and confidence intervals shown in Table G.2a. 
Delta Methylmercury TMDL Report G-4 

Table G.3a: Summary of Effluent 1 and Effluent 2 Methylmercury Concentrations 

FACILITY 

Footnotes EFF1 # of Samples

EFF1 

# of 

non-detects

Ave EFF1 

MeHg 

Conc 

(ng/l) (p)

Min EFF1 

MeHg 

Conc 

(ng/l) 

Max EFF1 

MeHg 

Conc 

(ng/l) 

 EFF2 # 

of 

Samples

EFF2 

# of 

non-detects

A

Aggregate 

Crystal Creek Aggregate a 1 1 0.010 0.01 0.01 

J.F. Shea CO Fawndale Rock and Asphalt a 1 1 0.010 0.01 0.01 1 1 

Lehigh Southwest Cement Co. a, b 1 1 0.010 0.01 0.01 1 1 

Oakwood Lake Subdivision Mining Reclamation a 2 1 0.027 0.01 0.043 

Aquaculture 

Calaveras Trout Farm (Rearing Facility) 2 0.060 0.027 0.092 

DFG Darrah Springs Fish Hatchery a, c 4 1 0.024 0.01 0.031 4 1 

DFG Merced River Fish Hatchery 1 0.037 0.037 0.037 

DFG Moccasin Creek Fish Hatchery a 1 1 0.010 0.01 0.01 

DFG Mokelumne River Fish Hatchery a 4 1 0.041 0.01 0.059 

DFG Nimbus Fish Hatchery 4 0.081 0.053 0.129 

DFG San Joaquin Fish Hatchery 2 0.060 0.047 0.073 

Pacific Coast Sprout Farms (Sacramento Facility) a 1 1 0.010 0.01 0.01 

UC Davis Center for Aquatic Biology & Aquaculture a, d 4 2 0.030 0.01 0.067 4 1 

USDI BR Winter Run Rearing Facility a 4 4 0.010 0.01 0.01 

USDI FWS Coleman Fish Hatchery 3 0.030 0.023 0.043 

Food 

Bell Carter Olive Company Inc. a 4 2 0.017 0.01 0.027 

CA Dairies, Inc. Los Banos Foods a 4 3 0.016 0.013 0.026 

Hershey Chocolate USA, Oakdale a 4 4 0.010 0.01 0.01 

Heating/Cooling 

CA State of, Central Heating/Cooling Facility a 4 3 0.015 0.01 0.029 

CALAMCO - Stockton Terminal 4 0.293 0.03 0.919 

Gaylord Container Corp. Antioch Pulp and Paper Mill 3 0.055 0.048 0.061 

Sacramento International Airport 2 0.035 0.023 0.046 

UA Local 38 Trust Fund Konocti Harbor Resort 1 0.079 0.079 0.079 

Manufacturing 

Formica Corporation Sierra Plant 1 0.050 0.05 0.05 

Proctor & Gamble Co. WWTP a, e 3 3 0.010 0.01 0.01 1 

 Mines 

Sliger Mine a 4 0.064 0.025 0.0909 
Delta Methylmercury TMDL Report G-5 

Table G.3a: Summary of Effluent 1 and Effluent 2 Methylmercury Concentrations 

FACILITY 

Footnotes EFF1 # of Samples

EFF1 

# of 

non-detects

Ave EFF1 

MeHg 

Conc 

(ng/l) (p)

Min EFF1 

MeHg 

Conc 

(ng/l) 

Max EFF1 

MeHg 

Conc 

(ng/l) 

 EFF2 # 

of 

Samples

EFF2 

# of 

non-detects

A

Misc 

DGS Office of State Publishing a, k 4 [3] 4 [3] 0.010 0.01 0.01 

South Feather Water & Power a, k 2 [1] 2 [1] 0.013 0.013 0.013 

UC Davis Hydraulics Laboratory 3 0.057 0.038 0.082 

Paper Mill 

Pactiv Molded Pulp Mill a 12 5 0.039 0.01 0.085 

SPI Anderson Division 4 0.106 0.036 0.14 2 

SPI Shasta Lake (Effluent 1 & 2) 1 0.023 0.023 0.023 1 

Stimpel Wiebelhaus Assoc. SWA at Mountain Gate 1 0.081 0.081 0.081 

POTW 

Aerojet Sacramento Facility f, k 1 (0) (k) (k) (k) 

Anderson WWTP a 12 2 0.090 0.01 0.271 

Atwater WWTP a 12 3 0.034 0.01 0.084 

Auburn WWTP a 12 6 0.028 0.01 0.072 

Bella Vista Water District 1 0.027 0.027 0.027 

Biggs WWTP 2 1.605 0.15 3.06 

Brentwood WWTP a 13 13 0.010 0.01 0.01 

Canada Cove LP French Camp Golf & RV Park 4 0.147 0.029 0.291 

Chico Regional WWTP 12 0.157 0.057 0.527 

Clear Creek CSD WWTP 2 0.036 0.028 0.043 1 

Colfax WWTP 3 0.197 0.115 0.35 

Colusa WWTP 4 2.863 1.97 4.02 

Corning Industries/ Domestic WWTP k 3 [2] 0.044 0.034 0.053 

Cottonwood WWTP 5 0.096 0.045 0.245 

Davis WWTP o 7 0.546 0.305 1.04 5 

Deer Creek WWTP a 13 11 0.015 0.013 0.032 

Deuel Vocational Institute WWTP a, k 4 [3] 4 [3] 0.010 0.01 0.01 

Discovery Bay WWTP a 12 7 0.191 0.013 2.03 

El Dorado Hills WWTP l 5 5 0.013 0.013 0.013 2 2 

Galt WWTP 6 0.139 0.027 0.22 

Grass Valley WWTP a 16 2 0.160 0.01 0.938 

Jackson WWTP 4 0.108 0.061 0.161 

Lincoln WWTP a, k 8 [7] 6 0.018 0.01 0.068 

Live Oak WWTP 4 0.591 0.427 0.785 
Delta Methylmercury TMDL Report G-6 

Table G.3a: Summary of Effluent 1 and Effluent 2 Methylmercury Concentrations 

FACILITY 

Footnotes EFF1 # of Samples

EFF1 

# of 

non-detects

Ave EFF1 

MeHg 

Conc 

(ng/l) (p)

Min EFF1 

MeHg 

Conc 

(ng/l) 

Max EFF1 

MeHg 

Conc 

(ng/l) 

 EFF2 # 

of 

Samples

EFF2 

# of 

non-detects

A

Lodi White Slough WWTP a, n 12 [10] 4 [3] 0.147 0.01 1.24 

Manteca WWTP 11 0.216 0.037 0.356 

Mariposa PUD WWTP 4 0.393 0.04 0.912 

Maxwell PUD WWTP 4 0.993 0.044 1.72 

Merced WWTP 12 0.386 0.13 0.672 

Modesto ID Regional WWTP k 3 [2] 0.056 0.045 0.066 

Modesto WWTP 4 0.125 0.109 0.161 1 

Nevada City WWTP a 4 2 0.048 0.01 0.146 

Nevada Co SD #1 Cascade Shores WWTP a 3 1 0.142 0.01 0.286 

Nevada Co SD #1 Lake Wildwood WWTP a 12 1 0.109 0.01 0.32 

Nevada Co SD #2 Lake of the Pines WWTP 2 1.409 0.708 2.11 

Olivehurst PUD WWTP a 13 1 0.144 0.013 0.268 

Oroville WWTP 12 0.147 0.061 0.28 

Paradise Irrigation District a 1 1 0.013 0.013 0.013 

Placer Co. SA #28 Zone #6 WWTP 2 0.668 0.474 0.862 

Placer Co. SMD #1 WWTP 12 0.141 0.042 0.35 Placer Co. SMD #3 WWTP 12 0.100 0.037 0.381 

Placerville Hangtown Creek WWTP a 12 1 0.058 0.013 0.17 

Planada Comm. Service Dist. WWTP 4 1.168 0.374 2.04 

Red Bluff WWTP a 12 6 0.030 0.01 0.057 

Redding Clear Creek WWTP a 12 3 0.042 0.013 0.084 

Redding Stillwater WWTP a 13 13 0.013 0.013 0.013 

Rio Alto WD- Lake CA WWTP 3 1.219 0.141 3.35 

Rio Vista Main WWTP 4 0.164 0.035 0.522 

Roseville Dry Creek WWTP a 12 4 0.023 0.01 0.055 

Roseville Pleasant Grove WWTP a 12 10 0.017 0.01 0.07 

San Andreas SD WWTP 4 0.249 0.178 0.293 

San Joaquin Co DPW - Flag City WWTP a 3 1 0.081 0.013 0.152 

Shasta Lake WTP a 2 1 0.025 0.01 0.04 

Shasta Lake WWTP a 2 1 0.022 0.01 0.034 

SRCSD Sacramento River WWTP 60 0.718 0.144 1.640 

SRCSD Walnut Grove WWTP (CSD1) k 3 [2] 2.155 0.949 3.36 

Stockton WWTP a 12 1 0.935 0.01 2.09 

Tracy WWTP a 13 1 0.145 0.013 0.422 
Delta Methylmercury TMDL Report G-7 

Table G.3a: Summary of Effluent 1 and Effluent 2 Methylmercury Concentrations 

FACILITY 

Footnotes EFF1 # of Samples

EFF1 

# of 

non-detects

Ave EFF1 

MeHg 

Conc 

(ng/l) (p)

Min EFF1 

MeHg 

Conc 

(ng/l) 

Max EFF1 

MeHg 

Conc 

(ng/l) 

 EFF2 # 

of 

Samples

EFF2 

# of 

non-detects

A

Tuolumne UD Sonora RWTP/ Jamestown SDWTP 3 0.182 0.071 0.262 

Turlock WWTP a, g 12 1 0.060 0.02 0.079 

UC Davis WWTP a 13 4 0.038 0.010 0.078 

United Auburn Indian Community Casino WWTP a 2 2 0.010 0.010 0.010 

Vacaville Easterly WWTP a 12 4 0.024 0.010 0.057 

West Sacramento WWTP a 12 1 0.050 0.010 0.085 

Williams WWTP 4 1.553 0.560 2.100 

Woodland WWTP a 12 2 0.031 0.013 0.059 

Yuba City WWTP 12 0.295 0.106 0.625 

Power 

Calpine Corp. Greenleaf Unit One Cogen Plant 4 0.064 0.02 0.117 

Camanche Dam Powerhouse a 4 3 0.020 0.01 0.039 

GWF Power Systems a 4 4 0.013 0.013 0.013 

Mirant Delta CCPP h 12 0.075 0.020 0.121 10 

Sacramento Cogen Authority Procter & Gamble Plant a 4 1 0.052 0.013 0.070 

SMUD Rancho Seco Nuclear Generating Station a 12 4 0.040 0.013 0.104 

Stockton Congeneration Co. a 4 3 0.017 0.013 0.029 

Wheelabrator Shasta Energy Co. 4 0.104 0.055 0.178 

WTP (GW) 

Aerojet Interim GW WTP a, k 2 [1] 2 [1] 0.013 0.013 0.013 2 [1] 2 [1] 

Boeing Company, Interim Treatment System a 1 1 0.010 0.01 0.01 

Defense Logistics Agency Sharpe GW Cleanup a, i 3 2 0.018 0.01 0.033 1 1 

General Electric Co. GWCS a, j, m 3 3 0.010 0.01 0.01 3 3 
Delta Methylmercury TMDL Report G-8 April 2010 

Table G.3a Footnotes: 

a. Sample MeHg concentration <MDL; half the detection limit was used for calculations. 

b. Lehigh Southwest Cement Co. Effluent 1: Outfall #1, Shale Quarry Tunnel Road. Effluent 2: Lehigh 

Southwest Cement Co., 002B: Shale Quarry 

c. Darrah Springs Fish Hatchery Effluent 1: Upper Springs. Effluent 2: Darrah Springs Fish Hatchery - 

Lower Springs 

d. UCD Center for Aquatic Biology & Aquaculture, Effluent 1: CABA Aquatic Center. Effluent 2: CABA 

Putah Creek Facility 

e. Proctor & Gamble, Pond Effluent 2: Effluent PTI-660 

f. Aerojet Sacramento facility, Effluent 1 sample collected from West Detention Pond because there 

was no discharge to the American River during the rainy season. 

g. City of Turlock WWTP, Effluent 1: (R5) 

h. Mirant Delta CCPP EFF 1:Outfall 001, Effluent 2: Outfall 002 

i. Defense logistics agency, Sharp GW Cleanup; Effluent 1: CBCGWTPEFF = Central area B/C Aquifer 

zone, Effluent 2: NBGWTPEFF = North GWTP effluent 

j. General Electric Co., GWCS: Effluent 1: Air Stripper Effluent, Effluent 2: 100-foot Zone Effluent 

k. Results for the following facilities and sample dates were not incorporated in the calculations due to 

sample preservation hold times exceeding EPA recommendations: Aerojet Interim GW WTP 

(18 November 2005, EFF 1 and EFF 2 were both <MDL); Aerojet Sacramento Facility (18 March 

2005, 0.057 ng/l); Corning Industries/ Domestic WWTP (22 September 2004, 0.041 ng/l); Deuel 

Vocational Institute WWTP (26 October 2004, <MDL); DGS Office of State Publishing (8 July 2005, 

<MDL); Lincoln WWTP (25 August 2005, 0.034 ng/l); Miners Ranch WTP (9 September 2004, 

<MLD);Modesto ID Regional WWTP (8 October 2004, 0.038 ng/l); and SRCSD Walnut Grove WWTP 

(CSD1) (29 December 2004, 0.759 ng/l). 

l. El Dorado Hills WWTP sampled effluent when discharging to land and to surface water. Only 

samples collected when the plant discharged to surface water (December 2004 through April 2005) 

were used in the summary. Effluent that was reclaimed during the seven warm season months 

ranged from nondetect to 0.055 ng/l, with one sample (9 August 2005, 0.057 ng/l) excluded due to 

sample preservation hold time exceeding EPA recommendations. 

m. General Electric Co. GWCS conducted four sampling events. However, results for General Electric 

Co. GWCS samples collected on 8 October 2004 were not incorporated in the calculations due to 

sample contamination with mercury in the laboratory. 

n. Lodi White Slough WWTP sampled effluent when discharging to land and to surface water. Only 

samples collected when the plant discharged to surface water (September 2004 through June 2005) 

were used in the summary. Effluent that was reclaimed in August 2004 and July 2005 had 

methylmercury concentrations of 0.054 ng/l and <MDL, respectively. 

o. Davis WWTP: Effluent 1: Willow Slough, Effluent 2: Conaway Ranch Toe Drain in the Yolo Bypass. 

p. Tables 6.5 and 8.4 in the main text of the TMDL Report and Tables B and C in the draft Basin Plan 

amendment provide average concentration values rounded to two decimal places using un-rounded 

Excel calculations, while this table provides values rounded to three decimal places. For example, 

the Tracy WWTP had an average methylmercury concentration of 0.014465 ng/l per the Excel 

calculations, which rounds to 0.0145 ng/l in this table, and 0.14 ng/l (not 0.15 ng/l) in Table 6.5. 
Delta Methylmercury TMDL Report G-9 

Table G.3b: Summary of Effluent 3 and Effluent 4 Methylmercury Concentrations 

FACILITY 

Footnotes 

EFF 3 

# of 

Samples 

EFF 3 

# of nondetects 

Ave EFF 3 

MeHg Conc 

(ng/l)

Min EFF 3 

MeHg Conc 

(ng/l)

Max EFF 3 

MeHg Conc 

(ng/l)

EFF 4 

# of Samples 

EFF 4 

# of nondetects 

Ave EFF 4 

MeHg Conc 

(ng/l)

Aggregate

Lehigh Southwest 

Cement Co. a, b 1 1 0.010 0.010 0.010 1 0.062 

Paper Mill

SPI Shasta Lake 

(Effluent 1 & 2) 1 0.485 0.485 0.485 

WTP (GW)

Aerojet Interim 

GW WTP a, e 2 [1] 2 [1] 0.013 0.013 0.013 2 [1] 2 [1] 0.013 

Defense Logistics 

Agency Sharpe 

GW Cleanup 

a, c 2 2 0.010 0.010 0.010 3 1 0.047 

General Electric 

Co. GWCS a, d 3 3 0.010 0.010 0.010 

a. Sample MeHg concentration <MDL; half the detection limit was used for calculations. b. Lehigh Southwest Cement Co., EFF 3: 001A: Limestone Quarry, EFF 4: 00X: Cement Plant c. Defense logistics agency, Sharp GW Cleanup, EFF 3: SBGWTPEFF= South GWTP effluent, EFF 4: SSJCUPST = South San Joaquin 

(upstream sample). 

d. General Electric Co. EFF 3: GWCS: Multizone Effluent 

e. Aerojet Interim GW WTP results for samples collected on 18 November 2005 (both <MDL) were not incorporated in the calculations due 

hold time exceeding EPA recommendations.

f. General Electric Co. GWCS conducted four sampling events. However, results for General Electric Co. GWCS samples collected on 8 

incorporated in the calculations due to sample contamination with mercury in the laboratory.
Delta Methylmercury TMDL Report G-10 

Table G.4: Available Intake and Outfall Methylmercury Concentration Data for Aquaculture, Power and Heating/Cooling F

Its Upstream Tributary Watersheds (a)

Facility 

[NPDES #, Type] 

Sample 

Date 

Outfall 1 

MeHg

Conc 

(ng/l) (b)

Outfall 1

MeHg

Qual. (b)

Outfall 2 

MeHg 

Conc 

(ng/l) 

Outfall 2

MeHg

Qual. (b)

Outfall 2 Field 

Dup 

MeHg 

Conc 

(ng/l) 

Outfall 2 Field 

Dup 

MeHg 

Qual. (b)

Intake 1 

MeHg 

Conc 

(ng/l) (a)

Intake 1

MeHg

Qual. (b)

Intake 

1 Dup. 

MeHg 

Conc 

(ng/l)

In

Q

CALAMCO - Stockton Terminal 

[CA0083968, Heating /Cooling] 8/26/04 0.030 B 0.026 B 

Calaveras Trout Farm 

(Rearing Facility) 

[CA0081752, Aquaculture] 

9/30/04 0.027 B 0.067 

Camanche Dam Powerhouse 

[CA0082040, Power] 1/19/2005 ND <MDL 0.095 (ba) 

DFG Darrah Springs 

Fish Hatchery 

[CA0004561, Aquaculture] 

9/15/04 0.029 B, (nn) 0.043 B, X, (mm) ND <MDL, (nn) 

DFG Mokelumne River 

Fish Hatchery 

[CA0004791, Aquaculture] 

11/16/04 0.048 A ND <MDL, A 0.020 <11/16/04 0.129 A 0.051 A 

2/17/05 0.053 

DFG Nimbus Fish Hatchery [CA0004774, Aquaculture] 

6/20/05 0.085 0.052 

DFG San Joaquin Fish Hatchery 

[CA0004812, Aquaculture] 9/28/04 0.073 0.021 B 

8/11/04 ND <MDL ND <MDL 11/4/04 ND <MDL ND <MDL 

2/3/05 ND <MDL 0.263 

GWF Power Systems 

[CA0082309, Power] 

5/5/05 ND <MDL ND <MDL 
Delta Methylmercury TMDL Report G-11 

Table G.4: Available Intake and Outfall Methylmercury Concentration Data for Aquaculture, Power and Heating/Cooling F

and Its Upstream Tributary Watersheds, continued

Facility 

[NPDES #, Type] 

Sample 

Date 

Outfall 1 

MeHg 

Conc 

(ng/l) (a)

Outfall 1

MeHg

Qual. (b)

Outfall 2 

MeHg 

Conc 

(ng/l) 

Outfall 2

MeHg

Qual. (b)

Outfall 

2 Field 

Dup 

MeHg 

Conc 

(ng/l) 

Outfall 2 Field 

Dup 

MeHg 

Qual. (b)

Intake 1 

MeHg 

Conc 

(ng/l) (a)

Intake 1

MeHg

Qual. (b)

Intake 

1 Dup. 

MeHg 

Conc 

(ng/l)

In

M

Q

2/4/04 0.081 0.0835 0.0799 (k) 0.296 (l) 3/3/04 0.116 0.127 0.12 (l) 0.122 8/3/04 0.020 J 0.070 ND <MDL 9/1/04 0.080 0.060 0.080 (l) 

10/5/04 0.049 B 0.060 0.038 (l), B 11/2/04 0.047 B 0.042 B 0.040 (l), B 12/2/04 0.030 B 0.063 0.070 (l) 1/11/05 0.083 0.081 0.102 (l) 

2/8/05 0.097 0.120 0.098 (l) 3/8/05 0.121 0.150 0.15 (l) 

4/26/05 0.083 Y 0.069 (l) 

Mirant Delta CCPP 

[CA0004863, Power] 

5/25/05 0.091 Y 0.077 (l) 

8/11/04 0.056 ND <MDL 10/6/04 0.069 ND <MDL 

1/5/05 0.070 0.080 

Sacramento Cogen Authority 

Procter & Gamble Plant 

[CA0083569, Power] 

5/4/05 ND <MDL ND <MDL 

(a) ND: nondetect (below method detection limit). Analytical method detection limits were 0.025 ng/l or less. (b) < MDL: below method detection limit; detection limits ranged between 0.020 and 0.025 ng/l. 

A: Samples were received out of optimal temperature range. B: Sample results above the MDL and below the ML; should be considered an estimate. J: Detected but below the reporting limit; result is an estimated concentration. X: Collected 9/14/04. Y: No discharge. (l): Mirant Delta CCPP Intake 002. (mm): Darrah Springs Fish Hatchery - Lower Springs. (nn): Darrah Springs Fish Hatchery - Upper Springs. (ba): Camache Dam Powerhouse receiving water received 200 feet upstream of discharge. 
Delta Methylmercury TMDL Report G-12 

Table G.5a: Available Intake and Outfall Total Mercury Concentration Data for Power and Heating/Cooling Facilities in t

Facility 

[NPDES #, Type] 

Proximity 

to Delta 

Sample 

Date 

Outfall 1 TotHg 

Conc. (ng/l) 

Outfall 2 TotHg

Conc. (ng/l) 

Intake 1 TotH

Conc. (ng/l) 

CALAMCO – Stockton Terminal (a)

[CA0083968, Heating/Cooling] 

Delta / 

Yolo Bypass 1/15/02 6.60 6.70 

5/27/04 6.40 6.70 6/17/04 7.00 7.60 7/19/04 9.10 10.00 8/26/04 3.50 3.80 9/23/04 3.80 2.60 

Gaylord Container Corp. 

Antioch Pulp and Paper Mill (a)

[CA0004847, Heating/Cooling] 

Delta / 

Yolo Bypass 

10/14/04 5.00 7.50 

3/28/2000 6.17 9.23 5.6 

12/11/2001 4.6 3.6 

7/9/2002 6.54 6.38 5/6/2003 6.29 

7/15/2003 7.88 8.42 

2/4/2004 3.69 4.21 (b) 2/9/2004 3.68 2.60 3/3/2004 9.15 8.19 8/3/2004 10.1 11.8 

Mirant Delta CCPP 

[CA0004863, Power] 

Delta / 

Yolo Bypass 

2/8/2005 1.6 4.25 

(a) The CALAMCO and Gaylord facilities no longer discharge to surface water. The Gaylord facility discharged non-contact cooling water from ope

It obtained its water from wells. 

(b) Average of field duplicates, 4.14 and 4.27 ng/l. 

Table G.5b: Mirant Delta CCPP Evaluation of Total Mercury Concentrations (ng/l) in Inputs to Its Discharge. 

Sample 

Date 

Demineralizer-Regeneration

Wastewater 

(Discharge to Outfall 1) 

Oil-Water Separator 

(Discharge to Outfall 1)

Reverse Osmosis 

Reject Water 

(Discharge to Outfall 1) 

Boiler Blowdown 

(Discharge to Outfall 2) 

E-0

S

(Disc

3/28/2000 7/24/2002 1.75 21.8 1.01 7/30/2002 69.0 10/9/2002 4.62 4.02 13.8 1.78 1/14/2003 6.73 6.09 5.65 5.19 
Delta Methylmercury TMDL Report G-13 

Table G.6: Description of Discharges from Power and Heating/Cooling Plants in the Delta Region. 

Agency 

(NPDES No.) 

Proximity 

to Delta 

Discharge

Volume

(mgd) Discharge Description 

Aerojet Sacramento 

Facility (CA0004111) 

Downstream 

of Dam 0.02 

The discharge contains stormwater, cooling tower overflow, boiler blowdown and some wastewaThe facility has 53 treated boilers, 12 non-treated boilers, 69 non-treated cooling towers, 13 treacooling towers, 56 evaporation condensers, and numerous other similar systems. Water is used cool rocket exhaust deflector plates during test firings. Wastewater may include water used to operate propellant vapor scrubbers when tanks are vented, and to draw a vacuum on propellantcontaminated components prior to disassembly. The Discharger states that this wastewater contains hydrazines, oxides of nitrogen, and N-nitrosodimethylamine. The wastewater is collectein a batch process, analyzed for compliance with effluent specifications and discharged to the sanitary sewer or Buffalo Creek, or if not meeting effluent limits, is either treated (neutralization achemical oxidation) for discharge or is hauled to a Class I disposal site. Maximum concentrationof treatment chemical in the boiler discharges (10 gallons per day [gpd]) are 40 ppm potassium hydroxide, 40 ppm dipotassium sulfite. Chemicals added to boilers and cooling towers: Betz Entec Opti-guard ACS or Betz Entec 

Optisperse 24; Betz Entrec 552 or Betz Entrec 367. 

California (State of) 

Central Heating/ 

Cooling facility 

Delta / 

Yolo Bypass 5.26 

Facility discharges closed-system cooling water. The heating of downtown State buildings is achieved through the use of boilers that do not discharge waste to surface waters. The Central Heating/Cooling Plant adds no chemicals to its cooling water. 

Calpine Corp. 

Greenleaf Unit One 

Cogen Plant 

(CA0081566) 

Downstream 

of Dam 0.11 

The discharger owns and operates a natural gas cogeneration plant that uses water for steam generation and cooling. The discharge consists of cooling water blowdown, which consists of 

reverse osmosis reject water, boiler blowdown, and condensed steam. The permit did not identthe water supply source for cooling water. Chemicals added to Cooling Water: Chlorine, Nalco 8305 Plus, Nalco 8300 dispersant, Nalco 

Stabrex ST40, sodium bisulfite solution, sodium hypochlorite solution, sulfuric acid, Nalco 1742, Nalco Elimin-Ox Oxygen Scavenger, Nalco Tri-act 1820 Inhibitor. 

East Bay Municipal 

Utility District 

Camache Dam 

Powerhouse 

(CA0082040) 

Downstream 

of Dam 0.04 

The discharger owns and operates an industrial wastewater collection, treatment, and disposal system at the Camanche Dam Power House. The facility obtains process water from the Mokelumne River. Within the powerhouse, drainage, washdown, and leakage waters that contalubricating oil and other petroleum products are collected in a sump, treated with a belt skimmerpumped to a separation/retention pond where additional oil is removed with a rope skimmer and series of separation baffles, and then discharged to the Mokelumne River. 

GWF Power Systems 

(CA0082309) 

Delta / 

Yolo Bypass 0.05 

The facility generates electrical power from the burning of petroleum coke as its primary fuel. Its discharge contains process wastewater from cooling tower blowdown, boiler blowdown, gland steam condensate, plant drains, reverse osmosis reject water and storm water. Water for coolinpurposes and steam production is obtained from the City of Antioch. Chemicals added: Sulfuric acid, Stabrex ST40 (microbiocide), dispersant, Phosperse-Plus 8309 

Inhibitor (corrosion inhibitor), and water conditioners. 
Delta Methylmercury TMDL Report G-14 

Table G.6: Description of Discharges from Power and Heating/Cooling Plants in the Delta Region. 

Agency 

(NPDES No.) 

Proximity 

to Delta 

Discharge

Volume

(mgd) Discharge Description 

Mirant CCPP 

(CA0004863) 

Delta / 

Yolo Bypass 123.93 

Discharge consists of non-cooling water and other low-volume waste streams resulting from the operation of the CCPP. Cooling water is drawn from the San Joaquin River. Waste streams to Outfall 1 include oil/water separator effluent [0.156 mgd], demineralization regeneration wastewa[0.0033 mgd], and reverse osmosis reject water [0.047 mgd]. Waste streams to Outfall 2 include boiler blowdown [0.030 mgd], boiler wastewater management system effluent [0.00165 mgd], cooling tower blowdown [3.63 mgd], HRSG blowdown [0.032 mgd], evaporative cooler blowdow[0.0324 mgd], and treatment chemicals [volume not available]. Chemicals added: Chlorine, sodium hypochlorite, sodium bromide, polyacrylate, sodium bisulfat

and terbuthlazine. 

SMUD Rancho Seco 

Nuclear Generating 

Station (CA0004758) 

Downstream 

of Dam 0.09 

Discharge contains stormwater, irrigation runoff, treated liquid radioactive wastewater, fire protection water, treated municipal wastewater, and dilution water from the Folsom South CanalThe facility plans to decrease the domestic wastewater effluent volume as the decommissioning process of the nuclear plant continues. Chemicals added: Sodium hypochlorite may be added to the retention basins for algae control. 

Wheelabrator Shasta 

Energy Co. 

(CA0081957) 

Downstream 

of Dam 0.02 

The Shasta facility is a wood-burning power plant and the Lassen facility is a natural gas fired plThe combined discharges from these plants contain cooling water, plant maintenance water, stowater runoff, groundwater from the “internal under drain” system, boiler blowdown, reject water from a reverse osmosis system, demineralization system backwash, fuel storage pile leachate aseepage, fly ash, bottom ash, waste petroleum products, and domestic waste. Firewater systemcooling, blowdown, maintenance, and drinking water are obtained from groundwater wells. Chemicals added: Sodium hydroxide (50%), sulphuric acid (93%), Drew Phos 2600, Amercor 87

Mekor 70, Cortrol OS7700, Vitec 3000, Conntect 5000 (engine cleaner detergent), ammonia, sodium hypochlorite solution, caustic soda liquid (25%), Drew 2215, DrewSperse, and HyperspeMSI 300. 

(a) Mercury data were not available for many of the added chemicals, especially the proprietary formulations for which lists of all product-specific ingredie

Potassium hydroxide and sodium hydroxide may be active ingredients in several of the formulations; see Table G.7. 
Delta Methylmercury TMDL Report G-15 

Table G.7: Mercury Concentrations in Chemicals Commonly Used at Power and Heating/Cooling Facilities. 

Chemicals Hg Concentration (a) Comment 

ammonia (NH3) 0.00243 ppb, 0.001 mg/l. The MASCO Mercury Database had two compound tes

hydroxide, a common commercial form of ammonia. 

bleach (not defined) 0.000568 ppb, 0.001 ppm caustic soda (50% membrane grade) 1 ppb caustic soda (50% solution) 1 ppb caustic soda (flake) 50 ppb caustic soda (water care grade) 0.5 ppm caustic soda liquid (25%) 0.5 ppm chlorine 535 ppm Chlorine is extracted from chlorides through oxidation a

compound test result in the MASCO Mercury Databaseconcentration of 535 ppm. 

hydrogen peroxide (H2O2, a.k.a. bleach) 0.0012 mg/L Oil (lubricating) 239-578 ng/l (LDGV), 

4.2 ng/l (HDDV) 

4 samples collected from three light-duty gasoline vehiccollected from one heavy-duty diesel vehicle (HDDV). 

phosphoric acid 0.0002 ppb potassium hydroxide 0.000212 ppb Potassium hydroxide may be an active ingredient in Na

Entec products. (b)

sodium bisulfate 0.010 ppm, 0.000208 ppb sodium bisulfite (solution) 0.001 mg/L sodium chloride (sodium salt) 0.001 mg/l (saline) sodium hydroxide 0.000624 ppb Sodium hydroxide may be an active ingredient in Nalco sodium hypochlorite (12.5% solution, a.k.a. bleach) <1 ppb to 20 ppb sulfuric acid (25% solution) 5 ppb sulfuric acid (50% solution) 2 to 10 ppb sulfuric acid (ACS Reagent) 5 ppb sulfuric acid (industrial) 0.05 mg/L sulfuric acid/sulphuric acid (% not defined) 0.0002 ppb, 0.3 ppb (a) All mercury concentration data were obtained from the MASCO Mercury Database (MASCO, 2008) except for the data for oil (Hoyer et al., 2002). U

this table are cited precisely as stated in these references. 

(b) Many of the products that facilities reported using are proprietary formulations for which lists of all product-specific ingredients are not publicly availa

Material Safety Data Sheets were available for some formulations. 
Delta Methylmercury TMDL Report G-16 April 2010 

Page intentionally left blank.
Delta Methylmercury TMDL Report H-1 April 2010 

H. URBAN RUNOFF CONSTITUENT CONCENTRATION DATA 

Figure H.1 Site Codes: 

1. Arcade Creek 

2. City of Sacramento Strong Ranch Slough 

3. City of Sacramento Sump 104 

4. City of Sacramento Sump 111 

5. Stockton Calaveras River Pump Station 

6. Stockton Duck Creek Pump Station 

7. Stockton Mosher Slough Pump Station 

8. Stockton Smith Canal Pump Station 

9. Tracy Drainage Basin 10 Outflow 

10. Tracy Drainage Basin 5 Outflow 

11. Tracy Lateral to Sugar Cut Slough 
Delta Methylmercury TMDL Report H-2 April 2010 

Figure H.1: Urban Runoff Constituent Concentrations. 

(Site codes are defined on the next page. Appendix L provides the raw data and data sources.)

A. Urban Runoff Methylmercury Concentration Data

0.0

0.2

0.4

0.6

0.8

1.0

0 1 2 3 4 5 6 7 8 9 10 11 12

Site Code

MeHg Conc (ng/l)

Dry Weather

Wet Weather

2.04 ng/l 

(dry weather)

1.213 ng/l 

(dry 

weather)

B. Urban Runoff Total Mercury Concentration Data

0

20

40

60

80

100

120

0 1 2 3 4 5 6 7 8 9 10 11 12

Site Code

TotHg Conc (ng/l)

1137.9 ng/l

578.0 ng/l

239.0 ng/l 

(wet weather

events)

C. Urban Runoff Total Suspended Solids Concentration Data

0

100

200

300

0 1 2 3 4 5 6 7 8 9 10 11 12

Site Code

TSS Conc (mg/l)

1,300 mg/l 

(wet weather event)
Delta Methylmercury TMDL Report H-3 April 2010 

Figure H.2: Pooled Urban Runoff Constituent Concentrations. 

Total Mercury Concentration Data

0

25

50

75

100

125

0123

Concentration (ng/l)

1 .13 7.9 ng/l

5 78.0 ng /l

2 39.0 ng /l

Dry

Weather

Wet

Weather

TSS Concentration Data

0

100

200

300

0123

Concentration (mg/l)

1,300 mg /l

Dry

Weather

Wet

Weather

Suspended Solids Hg Concentration 

(TotHg:TSS)

0.0

0.5

1.0

1.5

2.0

2.5

0123

Concentration (mg/kg)

19 mg/kg

5 .7 mg/ kg

14.1 mg /kg

6.0 mg /kg

Dry

Weather

Wet

Weather

Methylm ercury Concentration Data

0.0

0.3

0.6

0.9

0123

Concentration (ng/l)

A verag e

M edian

M M Hg Co nc

2.0 40 ng/l

1.2 13 ng/l

Wet

Weather

Dry

Weather
Delta Methylmercury TMDL Report H-4 April 2010 

Page intentionally left blank. 
Delta Methylmercury TMDL Report I-1 April 2010 

I. SUMMARY OF TOTAL MERCURY AND TSS CONCENTRATION DATA FOR MAJOR 

DELTA TRIBUTARY INPUT AND EXPORT LOADS 

This appendix is organized into six sections that provide the following information: 

1. Figures that summarize available total mercury and TSS concentration data for monitoring 

stations. 

2. Load and confidence interval calculation methods for tributary locations with statistically 

significant total mercury and/or TSS concentration/flow regressions and linear regression 

plots for the stations with statistically significant regressions. 

3. Load and confidence interval calculation methods for tributary sampling locations without 

statistically significant concentration/flow regressions. 

4. Error propagation calculation methods for the mass balances presented in Chapter 7. 

5. Figures that illustrate the regressions between total mercury and TSS concentrations used to 

calculate “Method B. Linear Regression Slope for Paired TotHg/TSS” cited in Table 7.17 for 

Delta inputs and exports. 

6. Tables that provide the regression-based annual mercury loads and sums of the three, five, 

and ten highest daily mercury loads in each water year for the Sacramento River at Freeport 

and Yolo Bypass at Prospect Slough. 

I.1 Total Mercury and TSS Concentration Time Series Plots 

Figure I.1a: Available Total Mercury Concentration Data for the Mokelumne River, Prospect 

Slough and San Joaquin River. 

Figure I.1b: Available TSS Concentration Data for the Mokelumne River, Prospect Slough and 

San Joaquin River. 

Figure I.2a: Available Total Mercury Concentration Data for the Sacramento River. 

Figure I.2b: Available TSS Concentration Data for the Sacramento River. 

Figure I.3a: Available Total Mercury Concentration Data for Small Westside and Eastside 

Tributaries. 

Figure I.3b: Available TSS Concentration Data for Small Westside and Eastside Tributaries. 

Figure I.4a: Available Total Mercury Concentration Data for Major Delta Exports. 

Figure I.4b: Available TSS Concentration Data for Major Delta Exports. 

Figure I.5a: Available Total Mercury Concentration Data for American River, Cache Creek, 

Colusa Basin & Feather River Watershed Outflow Locations. 

Figure I.5b: Available TSS Concentration Data for American River, Cache Creek, Colusa Basin 

& Feather River Watershed Outflow Locations. 

Figure I.6a: Available Total Mercury Concentration Data for Natomas East Main Drain, Putah 

Creek, Sacramento Slough (Sutter Bypass) & Sacramento River above Colusa 

Watershed Outflow Locations. 

Figure I.6b: Available TSS Concentration Data for Natomas East Main Drain, Putah Creek, 

Sacramento Slough (Sutter Bypass) & Sacramento River above Colusa Watershed 

Outflow Locations. 
Delta Methylmercury TMDL Report I-2 April 2010 

Figure I.1a: Available Total Mercury Concentration Data for the Mokelumne River, 

Prospect Slough and San Joaquin River. 

Mokelumne River near I-5

0

5

10

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

Total Hg Conc. (ng/L)

San Joaquin River

0

5

10

15

20

25

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

Total Hg Conc. (ng/L)

Prospect Slough

0

25

50

75

100

125

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

Total Hg Conc. (ng/L)

Sam ples co llected during tidedo minated flo w co nditio ns

Sam ples co llected during net

Yo lo B ypass o utflo w

1/10/95: 695.6 ng/l

1/11/95: 553.7 ng/l
Delta Methylmercury TMDL Report I-3 April 2010 

Figure I.1b: Available TSS Concentration Data for the Mokelumne River, 

Prospect Slough and San Joaquin River. 

Mokelumne River near I-5

0

10

20

30

40

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

San Joaquin River

0

50

100

150

200

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Prospect Slough

0

125

250

375

500

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Sam ples co llected during tidedo m inated flo w co nditio ns

Sam ples co llected during net Yo lo

B ypass o utflo w

1/10/95: 2300.7 m g/l

1/11/95: 1454.4 m g/l
Delta Methylmercury TMDL Report I-4 April 2010 

Figure I.2a: Available Total Mercury Concentration Data for the Sacramento River. 

Sacramento River at Freeport

0

10

20

30

40

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

Total Hg Conc. (ng/L)

Sacramento River at Greene's Landing

0

20

40

60

80

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

Total Hg Conc. (ng/L)

Sacramento River at River Mile 44

0

10

20

30

40

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

Total Hg Conc. (ng/L)

12/6/94: 73.4 ng/l
Delta Methylmercury TMDL Report I-5 April 2010 

Figure I.2b: Available TSS Concentration Data for the Sacramento River. 

Sacramento River at Freeport

0

100

200

300

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03 Oct-04

TSS Conc. (mg/l)

1/15/98: 368 mg/l

Sacramento River at River Mile 44

0

100

200

300

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Sacramento River at Greene's Landing

0

100

200

300

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03 Oct-04

TSS Conc. (mg/l)

1/10/95: 374 mg/l

1/11/95: 327 mg/l
Delta Methylmercury TMDL Report I-6 April 2010 

Figure I.3a: Available Total Mercury Concentration Data for Small Westside 

and Eastside Tributaries. 

Small Westside Tributaries

0

20

40

60

80

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

Marsh Creek

Ulatis Creek

Small Eastside Tributaries: Sacramento Region

0

5

10

15

20

25

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

Morrison Creek @ Franklin

Morrison Creek @ I-5

Morrison Creek d/s UPRR

Morrison Creek u/s Meadow lark Lake

Small Eastside Tributaries: Stockton Region

0

15

30

45

60

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc (ng/l)

Bear Creek (Stockton)

Calaveras River

French Camp Slough

Mosher Creek
Delta Methylmercury TMDL Report I-7 April 2010 

Figure I.3b: Available TSS Concentration Data for Small Westside 

and Eastside Tributaries.

Small Westside Tributaries

0

200

400

600

800

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Marsh Creek

Ulatis Creek

Small Eastside Tributaries: Sacramento Region

0

40

80

120

160

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Morrison Creek @ Franklin

Morrison Creek @ I-5

Morrison Creek d/s UPRR

Morrison Creek u/s Meadow lark Lake

Small Eastside Tributaries: Stockton Region

0

50

100

150

200

250

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Bear Creek (Stockton)

Calaveras River

French Camp Slough

Mosher Creek
Delta Methylmercury TMDL Report I-8 April 2010 

Figure I.4a: Available Total Mercury Concentration Data for Major Delta Exports. 

Delta Mendota Canal

0

2

4

6

8

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/L)

Outflow to SF Bay (X2)

0

10

20

30

40

50

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/L)

State Water Project

0

2

4

6

8

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/L)
Delta Methylmercury TMDL Report I-9 April 2010 

Figure I.4b: Available TSS Concentration Data for Major Delta Exports. 

Delta Mendota Canal

0

10

20

30

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

State Water Project

0

15

30

45

60

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Outflow to SF Bay (X2)

0

45

90

135

180

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)
Delta Methylmercury TMDL Report I-10 April 2010 

Figure I.5a: Available Total Mercury Concentration Data for American River, 

Cache Creek, Colusa Basin & Feather River Watershed Outflow Locations.

A merican River

0

5

10

15

20

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

Cache Creek Settling Basin Outflow

0

300

600

900

1,200

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

Colusa Basin Drain

0

15

30

45

60

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

Feather River

0

15

30

45

60

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)
Delta Methylmercury TMDL Report I-11 April 2010 

 Figure I.5b: Available TSS Concentration Data for American River, Cache Creek, 

Colusa Basin & Feather River Watershed Outflow Locations. 

A merican River at Discovery Park

0

20

40

60

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

1/10/97: 116 mg/l

Cache Creek Settling Basin Outflow

0

500

1000

1500

2000

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Colusa Basin Drain

0

100

200

300

400

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Feather River

0

40

80

120

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)
Delta Methylmercury TMDL Report I-12 April 2010 

Figure I.6a: Available Total Mercury Concentration Data for Natomas East Main Drain, 

Putah Creek, Sacramento Slough (Sutter Bypass) & Sacramento River above Colusa 

Watershed Outflow Locations.

Putah Creek

0

50

100

150

200

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

3/9/95: 485 mg/l

Sacramento River at Colusa

0

30

60

90

120

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

Sacramento Slough

0

10

20

30

40

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc. (ng/l)

Natomas East Main Drain Watershed

0

20

40

60

80

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TotHg Conc (ng/l)

A rcade Creek @ Norw ood A ve.

A rcade Creek nr Del Paso Heights

Dry Creek
Delta Methylmercury TMDL Report I-13 April 2010 

Figure I.6b: Available TSS Concentration Data for Natomas East Main Drain, 

Putah Creek, Sacramento Slough (Sutter Bypass) & 

Sacramento River above Colusa Watershed Outflow Locations. 

Sacramento River at Colusa

0

200

400

600

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Sacramento Slough

0

50

100

150

200

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

Putah Creek

0

50

100

150

200

250

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc. (mg/l)

2/18/04: 418 mg/l

Natmos East Main Drain Watershed

0

40

80

120

Oct-93 Oct-94 Oct-95 Oct-96 Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03

TSS Conc (mg/l)

A rcade Creek @ Norw ood A ve.

A rcade Creek nr Del Paso Heights
Delta Methylmercury TMDL Report I-14 April 2010 

I.2 Average Annual Load and Confidence Interval Calculations for Tributary Sampling 

Stations with Statistically Significant Concentration / Flow Regressions 

Staff predicted the concentration of total mercury and/or TSS from flow for tributary sampling 

stations with significant (P < 0.05) concentration/flow linear regressions (Table I.1 and 

Figures I.7a and I.7b). Daily mercury and/or TSS concentrations were predicted for each 

tributary for two periods: WY2000-2003 and WY1984-2003. Daily loads were calculated using 

daily average flow data (Appendix E). Average annual loads were calculated using 

Equation I.1. 

Equation I.1: 

Average Annual Load = 

 Where: 

H = Number of years being averaged (20 or 4 years) 

i c = Constant of proportionality 

* Y = Average concentration (i.e. Total mercury or TSS) of the 

 data used for the regression 

1 b = Slope derived from the linear regression 

Xi = Daily average flow (cfs) from the flow record for 20 or 4 years 

* X = Average of the daily average flow of the data used for the regression 

 

The variance of the average annual loads was calculated from Equation I.2. 

Equation I.2:

 Variance (s2

) = 

 Where: 

 H = Number of years being averaged (20 or 4 years) 

 i c = Constant of proportionality 

2 σ = Residual mean square (MSE) from the regression 

* n = Sampled population size of the data on which the regression was based 

 Xi = Daily average flow (cfs) from the flow record for 20 or 4 years 

 * Xi = Daily average flow (cfs) of the data used for the regression 

 * X = Average of the daily average flow of the data used for the regression 

)( 1 * 1 * XXc

H

b Yc

H i + ∑∑ ii −

( ) ⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

− ⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛ − +⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛ ⎟

⎠

⎞ ⎜

⎝

⎛

∑

∑ ∑ 2**

2

2 *

*

2

2

2

)(

1 )(

H XX

XXc

n

c

H i

ii

i

σ σ
Delta Methylmercury TMDL Report I-15 April 2010 

From the variance, standard error was calculated using Equation I.3. 

Equation I.3:

 Standard Error (SE) = ( )

2/1

*

2

2 ⎟

⎠

⎞ ⎜

⎝

⎛

n − s

 Where: 

 2

s = Variance calculated by Equation I.2 

 * n = Sampled population size of the data on which the regression was based 

Using the above standard error, the confidence interval was calculated from Equation I.4. 

Equation I.4:

 Confidence Interval (CI) = Average Annual Load ± df ×tSE α, 

 Where: 

 SE = Standard error calculated by Equation I.3 

 df tα , = Critical t-value with the probability (α) of 0.05 and ( * n -2) degrees of 

freedom 

This method was developed by Professor Neil Willits (Willits, 2005-2006) at the University of 

California at Davis. All calculations were made using Microsoft Excel’s Data Analysis ToolPak. 

The method for calculating average annual loads and confidence intervals for tributary sampling 

stations without statistically significant concentration/flow regressions is described in Section J.3 

after Table I.1 and Figures I.7a and 7.b. 
Delta Methylmercury TMDL Report I-16 April 2010 

Table I.1: Statistical Significance of Linear Regressions Between Concentration and Daily Flow 

at Tributary and Export Sampling Stations. 

Sampling Stations (a)

Total Mercury/Flow 

Regression Statistically 

Significant (P < 0.05) 

TSS/Flow Regression 

Statistically Significant 

(P < 0.05) 

Delta Imports 

American River at Discovery Park Yes Yes 

Cache Creek d/s Settling Basin Yes Yes 

Colusa Basin Drain Yes Yes 

Feather River Yes Yes 

Mokelumne River d/s I-5 No No 

Putah Creek at Mace Blvd Yes Yes 

Sacramento River at Colusa Yes Yes 

Sacramento River at Freeport Yes Yes 

San Joaquin River at Vernalis No No 

Marsh Creek Yes No 

Prospect Slough (Yolo Bypass) Yes Yes 

Delta Exports 

Export to San Francisco Bay Delta (X2 and Chipps Island) No No 

Delta Mendota Canal at Byron Highway No No 

State Water Project at Bethany Reservoir No No 

(a) Bear, Mosher, Morrison and Ulatis Creeks, Calaveras River, Natomas East Main Drain, and French Camp Slough tributary 

stations were not evaluated because there are no flow gages near the stations. The flow gage near the Sacramento Slough 

station is not rated for high flows and is therefore not adequate for this analysis. 
Delta Methylmercury TMDL Report I-17 April 2010 

Figure I.7a: Total Mercury Concentration versus Daily Flow for Tributary Inputs with 

Statistically Significant (P < 0.05) Linear Regressions. 

American River

y = 0.0003x + 1.7331

R2 = 0.2877

0.00

5.00

10.00

15.00

20.00

0 10,000 20,000 30,000 40,000

Flow (cfs)

TotHg Conc. (ng/L)

Cache Creek

y = 0.0403x

R2 = 0.8214

0

400

800

1,200

0 5,000 10,000 15,000 20,000

Flow (cfs)

TotHg Conc. (ng/L)

Sacramento River @ Freeprot

y = 0.0002x + 2.8207

R2 = 0.4437

0

10

20

30

40

0 40,000 80,000 120,000

Flow (cfs)

TotHg Conc. (ng/L)

Feather River

y = 0.0002x + 4.9386

R2 = 0.2559

0

15

30

45

60

0 30,000 60,000 90,000 120,000

Flow (cfs)

TotHg Conc. (ng/L)

Colusa Basin Drain

y = 0.0028x + 8.1535

R2 = 0.1839

0

20

40

60

80

0 4,000 8,000 12,000 16,000

Flow (cfs)

TotHg Conc. (ng/L)

Marsh Creek

y = 0.7352x + 1.9596

R2 = 0.7189

0

10

20

30

40

0 10 20 30 40 50

Flow (cfs)

TotHg Conc. (ng/L)

Prospect Slough

y = 0.0002x + 22.185

R2 = 0.3388

0

25

50

75

100

0 40000 80000 120000 160000

Flow (cfs)

TotHg Conc. (ng/L)

Sacrameto River @ Colusa

y = 0.001x

R2 = 0.5169

0

30

60

90

120

0 15,000 30,000 45,000 60,000

Flow (cfs)

TotHg Conc. (ng/L)

Putah Creek

y = 0.0053x + 7.653

R2 = 0.3187

0

25

50

75

100

125

150

0 2000 4000 6000 8000 10000 Flow (cfs)

TotHg Conc. (ng/L)

Cache Creek d/s Settling Basin 

Cache Creek u/s Settling Basin

y = 0.0775x - 24.057

R2

 = 0.8339

0

500

1000

1500

2000

2500

0 5000 10000 15000 20000

Flow (cfs)

TotHg Conc. (ng/L)

Putah Creek

y = 0.0053x + 7.653

R2 = 0.3187

0

25

50

75

100

125

150

0 2000 4000 6000 8000 10000 Flow (cfs)

TotHg Conc. (ng/L)
Delta Methylmercury TMDL Report I-18 April 2010 

Putah Creek

y = 0.0238x + 24.1

R2 = 0.488

0

150

300

450

600

0 2,500 5,000 7,500 10,000

Flow (cfs)

TSS Conc. (mg/L)

Sacramento River @ Colusa

y = 0.009x

R2 = 0.6054

0.00

200.00

400.00

600.00

800.00

0 15,000 30,000 45,000 60,000

Flow (cfs)

TSS Conc. (mg/L)

Sacramento River @ Freeport

y = 0.0009x + 9.7131

R2 = 0.2986

0

100

200

300

400

0 25,000 50,000 75,000 100,000

Flow (cfs)

TSS Conc. (mg/L)

Prospect Slough

y = 0.0016x + 104.2

R2 = 0.4403

0.0

200.0

400.0

600.0

800.0

0 40000 80000 120000 160000

Flow (cfs)

TSS Conc. (mg/L)

American River

y = 0.0015x

R2 = 0.4584

0.000

30.000

60.000

90.000

120.000

0 10,000 20,000 30,000 40,000

Flow (cfs)

TSS Conc. (mg/L)

Cache Creek

0

200

400

600

800

1000

1200

1400

1600

1800

2000

0 5,000 10,000 15,000 20,000 25,000

Flow (cfs)

TSS Conc. (mg/L)

Colusa Basin Drain

y = 0.0315x + 94.38

R2 = 0.2341

0

150

300

450

600

0 2,500 5,000 7,500 10,000

Flow (cfs)

TSS Conc. (mg/L)

Feather River

y = 0.0005x + 17.712

R2 = 0.167

0

40

80

120

160

0 40,000 80,000 120,000

Flow (cfs)

TSS Conc. (mg/L)

Figure I.7b: TSS Concentration versus Daily Flow for Tributary Inputs with Statistically 

Significant (P < 0.05) Linear Regressions. 
Delta Methylmercury TMDL Report I-19 April 2010 

( )( ) ( ) .... 2 2 2

1 2 3 SEload + SEload + SEload +

I.3 Annual Average Load and Confidence Interval Calculations for Tributary Sampling 

Stations without Statistically Significant Concentration / Flow Regressions 

For the tributary and export sampling locations where linear regressions were not statistically 

significant (P < 0.05, see Table I.1), the daily loads for total mercury and TSS were calculated 

by multiplying the mean concentration for the sampled data by each water bodies’ daily flow for 

two different periods: WY2000-2003 and WY1984-2003. Then the daily loads were summed 

(1461 days for 4 years or 7305 days for 20 years) and divided by the appropriate number of 

years to determine the average annual loads for each period. If the flow record was missing or 

unavailable for any number of days, then the sums of the daily loads were normalized to 7305 

days for 20 years or 1461 days for 4 years before dividing by the number of years. For 

example, a 20-year record would be normalized by dividing 7305 (the number of days in the 20-

year period) by the number of days with a recorded value in the flow record and then multiplying 

the resulting quotient by the calculated sum of loads; the result was then divided by 20 to obtain 

the average annual load. 

To determine the upper and lower confidence intervals for the annual loads, the upper and 

lower 95% confidence limits of the concentration means, respectively, were multiplied by each 

water bodies’ daily flow for 20 and 4 years, summed, and divided by the appropriate number of 

years. 

The sampled data’s concentration mean, standard error, and 95% confidence interval were 

calculated using the Microsoft Excel Data Analysis ToolPak option, “Descriptive Statistics”. 

I.4 Calculations for Error Propagation for the Mass Balances 

To determine the confidence intervals of the mass balance components (i.e., sum of input loads 

or sum of export loads), staff determined the propagated error of the summed loads using 

Equation I.5 and the confidence interval for the summed loads using Equation I.6. This method 

was developed by Professor Neil Willits (Willits, 2005-2006) at the University of California at 

Davis. All calculations were made using Microsoft Excel’s Data Analysis ToolPak. 

Equation I.5: 

 Standard Error of Summed Loads (SEall) = 

Equation I.6: 

 Confidence Interval of the Summed Loads (CIall) = Summed Loads ± *

all ,df × tSE α

 Where:

 SEall = Standard error calculated in Equation I.5 

*

,df tα = Critical t-value with the probability () of 0.05 and (nall-1) degrees of freedom. 

 nall = ∑( +++ ....) * * *

1 2 3 load load load nnn
Delta Methylmercury TMDL Report I-20 April 2010 

I.5 Regressions between Total Mercury and TSS Concentrations for Delta Inputs 

and Exports 

Figure I.8: TotHg:TSS Regressions for Delta Inputs 

Figure I.9: TotHg:TSS Regressions for Tributary Inputs to the Sacramento Basin 

Figure I.10: TotHg:TSS Regressions for Delta Exports 
Delta Methylmercury TMDL Report I-21 April 2010 

 

Figure I.8a: TotHg:TSS Regressions for Delta Inputs 

Mokelumne River

y = 0.372x

R2 = 0.4438

0

5

10

15

0 10 20 30 40

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Bear/Mosher Creeks

y = 0.0665x

R2 = -1.9742

0

5

10

15

0 50 100 150 200 250

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Calaveras River 

y = 0.1698x

R2 = -5.0185

0

10

20

30

40

0 50 100 150 200

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

French Camp Slough

y = 0.6309x

R2 = -0.0717

0

20

40

60

0 10 20 30 40 50

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Marsh Creek

y = 0.1239x

R2 = 0.2782

0

10

20

30

40

0 100 200 300

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Morrison Creek

y = 0.1521x

R2 = 0.4735

0

10

20

30

0 50 100 150

TSS Concentration (mg/l)

TotHg Concentration (ng/l)
Delta Methylmercury TMDL Report I-22 April 2010 

 Figure I.8b: TotHg:TSS Regressions for Delta Inputs 

Prospect Slough (Yolo Bypass) 

y = 0.1762x

R2 = 0.7054

0

25

50

75

100

0 200 400 600

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Sacramento River (Freeport)

y = 0.1681x

R2 = 0.4308

0

20

40

60

80

0 100 200 300 400

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

San Joaquin River

y = 0.1314x

R2 = 0.7535

0

10

20

30

0 50 100 150 200

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Ulatis Creek

y = 0.1114x

R2 = 0.1289

0

25

50

75

100

0 200 400 600 800 1,000

TSS Concentration (mg/l)

TotHg Concentration (ng/l)
Delta Methylmercury TMDL Report I-23 April 2010 

 Figure I.9a: TotHg:TSS Regressions for Tributary Inputs to the Sacramento Basin 

American River 

y = 0.1971x

R2 = -0.1639

0

10

20

30

0 50 100 150

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Cache Creek Settling Basin 

y = 0.484x

R2 = 0.9273

0

400

800

1,200

0 500 1,000 1,500 2,000

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Colusa Basin Drain 

y = 0.0866x

R2 = 0.4216

0

20

40

60

80

0 200 400 600

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Feather River 

y = 0.2577x

R2 = 0.5292

0

20

40

60

0 50 100 150

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Arcade Creek

y = 0.3806x

R2 = -0.5558

0

10

20

30

40

0 50 100 150

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Putah Creek 

y = 0.2584x

R2 = 0.916

0

40

80

120

160

0 100 200 300 400 500

TSS Concentration (mg/l)

TotHg Concentration (ng/l)
Delta Methylmercury TMDL Report I-24 April 2010 

Figure I.9b: TotHg:TSS Regressions for Tributary Inputs to the Sacramento Basin 

 Figure I.10: TotHg:TSS Regressions for Delta Exports 

Sacramento River above Colusa

y = 0.1203x

R2 = 0.8643

0

40

80

120

0 200 400 600 800

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Sacramento Slough

y = 0.1264x

R2 = 0.2688

0

10

20

30

40

0 50 100 150 200

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

Delta Mendota Canal

y = 0.1645x

R2 = 0.1392

0

2

4

6

8

0 10 20 30 40

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

X2

y = 0.2998x

R2 = 0.9569

0

20

40

60

0 50 100 150 200

TSS Concentration (mg/l)

TotHg Concentration (ng/l)

State Water Project

y = 0.1753x

R2 = -0.0283

0

5

10

15

0 20 40 60 80

TSS Concentration (mg/l)

TotHg Concentration (ng/l)
Delta Methylmercury TMDL Report I-25 April 2010 

I.6 Regression-based Annual and Highest Daily Mercury Loads for the 

Sacramento Basin 

Table I.2 provides the regression-based annual mercury loads and sums of the three, five, and 

ten highest daily mercury loads in each water year for the Sacramento River at Freeport, Yolo 

Bypass at Prospect Slough, and total Sacramento Basin outflows (Sacramento River + Yolo 

Bypass). The daily and annual loads were calculated using the daily total mercury 

concentrations predicted by the concentration/flow regressions described in Section J.2 and 

daily average flow data for WY1984-2003 described in Appendix E. 
Delta Methylmercury TMDL Report I-26 

Table I.2: Regression-based Annual Mercury Loads and Sums of the Three, Five, and Ten Highest Daily Mercury 

Water Year for Sacramento Basin Outflows. 

A. Sacramento River @ Freeport B. Yolo Bypass @ Prospect Slough C. Sacramento Basi

Water 

Year 

Annual 

TotHg 

Load 

(kg/yr) 

Sum of 

3 

Highest 

Daily 

Loads 

(kg) 

Sum of 

5 

Highest 

Daily 

Loads 

(kg) 

Sum of

10 

Highest

Daily 

Loads 

(kg) 

Water

Year 

Annual

TotHg

Load 

(kg/yr) 

Sum of

3 Highest 

Daily 

Loads

(kg) 

Sum of

5 

Highest 

Daily 

Loads

(kg) 

Sum of 

10 

Highest 

Daily 

Loads 

(kg) 

Water

Year 

Annual

TotHg

Load 

(kg/yr) 

Sum of

3 Highest 

Daily 

Loads

(kg) 

1984 268 11 18 34 1984 230 92 131 168 1984 497 103 1985 85 3 4 9 1985 3 1 1 1 1985 88 3 1986 212 15 24 43 1986 833 355 491 628 1986 1045 370 1987 59 2 4 7 1987 0 0 0 0 1987 59 3 1988 57 2 4 7 1988 2 1 1 2 1988 59 3 1989 93 7 10 19 1989 1 0 1 1 1989 94 7 1990 56 2 3 5 1990 0 0 0 0 1990 56 2 1991 40 3 5 8 1991 1 1 1 1 1991 41 4 1992 47 3 6 10 1992 2 1 1 2 1992 49 4 1993 219 9 15 29 1993 61 12 20 33 1993 280 21 1994 54 2 3 5 1994 0 0 0 0 1994 54 2 1995 385 12 20 37 1995 600 121 188 301 1995 985 131 1996 266 10 17 32 1996 122 26 39 60 1996 388 36 1997 269 14 22 42 1997 704 279 382 498 1997 972 294 1998 391 11 17 33 1998 408 73 114 187 1998 799 83 1999 248 10 16 30 1999 43 7 11 19 1999 291 16 2000 194 10 16 31 2000 102 15 25 45 2000 296 24 2001 65 3 5 9 2001 4 1 1 2 2001 69 4 2002 100 6 10 18 2002 14 5 6 9 2002 114 11 2003 179 6 10 20 2003 24 4 6 8 2003 203 10 

(a) The predicted daily mercury loads for the Sacramento River at Freeport and Yolo Bypass at Prospect Slough were summed by date to estima

from the Sacramento Basin and then ranked within each water year to determine the highest three, five and ten daily loads in each water yea

Basin. As a result, the highest daily loads in (C) may not equal the sum of the highest daily loads in (A) and (B). 
Delta Methylmercury TMDL Report J-1 

J. 2002 ANNUAL TOTAL MERCURY LOADS FROM AIR EMISSION FACILITIES THAT REPORT

CALIFORNIA AIR RESOURCES BOARD (ARB, 2003) 

FACILITY TYPE / 

TOTAL MERCURY 

LOAD (kg) 

American 

River 

below 

Folsom 

Dam 

Bear 

Creek, 

Fresno R. 

& San 

Joaquin R. 

abv Res. 

Butte 

Creek / 

Sutter 

Bypass

Cache 

Creek

Colusa 

Basin 

Coon 

Creek 

& 

Cross 

Canal Delta 

Feather 

River 

below 

Oroville 

Dam 

Morrison 

Creek 

Natomas

East 

Main 

Drain &

Arcade

Creek 

Putah - 

Cache 

Lowlands 

Sacramento 

River 

abv 

Colusa

Sacra

ment

Rive

abv 

Keswi

Dam 

ANIMAL & MARINE 

FATS AND OILS 4.048 

BEET SUGAR 1.438 

BRICK AND 

STRUCTURAL CLAY 

TILE 

 0.006 

CANNED FRUITS 

AND VEGETABLES 0.00026 

CANNED 

SPECIALTIES 

CEMENT, 

HYDRAULIC 35.337 

CHOCOLATE AND 

COCOA PRODUCTS 

COLLEGES & 

UNIVERSITIES, NEC 0.002 

COMMERCIAL 

PRINT / 

LITHOGRAPH 

 0.803 

CONCRETE 

PRODUCTS, NEC 10.579 

CONSTRUCTION 

SAND AND GRAVEL 0.004 2.275 0.104 0.00005 

CORRECTIONAL 

INSTITUTIONS 

COTTON GINNING 

COTTONSEED OIL 

MILLS 

CROP 

PREPARATION 

SVCS FOR MKT 

 0.001 0.006 0.001 0.003 
Delta Methylmercury TMDL Report J-2 

FACILITY TYPE / 

TOTAL MERCURY 

LOAD (kg) 

American 

River 

below 

Folsom 

Dam 

Bear 

Creek, 

Fresno R. 

& San 

Joaquin R. 

abv Res. 

Butte 

Creek / 

Sutter 

Bypass

Cache 

Creek

Colusa 

Basin 

Coon 

Creek 

& 

Cross 

Canal Delta 

Feather 

River 

below 

Oroville 

Dam 

Morrison 

Creek 

Natomas

East 

Main 

Drain &

Arcade

Creek 

Putah - 

Cache 

Lowlands 

Sacramento 

River 

abv 

Colusa

Sacra

ment

Rive

abv 

Keswi

Dam 

CRUSHED AND 

BROKEN STONE, 

NEC 

 0.018 

DRILLING AND OIL 

AND GAS WELLS 0.003 

ELECTRIC & OTHER 

SERVICES COMB 9.934 4.193 0.324 0.658 

ELECTRIC 

SERVICES 3.656 

FOOD 

PREPARATIONS, 

NEC 

 1.313 

FUNERAL SERVICE 

& CREMATORIES 1.643 0.617 7.194 2.343 2.801 

GENERAL 

MED/SURGICAL 

HOSPITALS 

0.00042 0.00011 

GLASS 

CONTAINERS 

GUIDED MISSILES 

AND SPACE VEH 0.00025 

INDUSTRIAL 

ORGANIC CHMLS, 

NEC 

 0.00005 

LAMINATED 

PLSTCS PLATE & 

SHEET 

 0.025 

LAND MINERAL 

WILDLIFE CONSERV 0.006 

MILLWORK 0.018 

MISC 

NONMETALLIC 

MINERALS 

 0.053 

NATIONAL 

SECURITY 0.000 13.041 0.001 
Delta Methylmercury TMDL Report J-3 

FACILITY TYPE / 

TOTAL MERCURY 

LOAD (kg) 

American 

River 

below 

Folsom 

Dam 

Bear 

Creek, 

Fresno R. 

& San 

Joaquin R. 

abv Res. 

Butte 

Creek / 

Sutter 

Bypass

Cache 

Creek

Colusa 

Basin 

Coon 

Creek 

& 

Cross 

Canal Delta 

Feather 

River 

below 

Oroville 

Dam 

Morrison 

Creek 

Natomas

East 

Main 

Drain &

Arcade

Creek 

Putah - 

Cache 

Lowlands 

Sacramento 

River 

abv 

Colusa

Sacra

ment

Rive

abv 

Keswi

Dam 

NITROGENOUS 

FERTILIZERS 

PAPER MILLS 0.577 

PAVING MIXTURES 

AND BLOCKS 0.030 0.045 0.079 5.382 

PLASTICS 

MATERIALS AND 

RESINS 

 0.00010 

PREPARED FEEDS, 

NEC 0.00132 

RICE MILLING 0.0006 0.014 0.00093 0.001 

SANITARY 

SERVICES, NEC 2.050 

SAWMILLS & 

PLANING MILLS, 

GNL 

 0.005 0.068 3.062 

SEMICONDUCTORS

/RELATED DEVICES 0.002 

VEGETABLES OIL 

MILLS, NEC 0.00059 

VET SERV, 

SPECIALISTS 0.009 0.232 

Grand Total 5.714 0.030 0.005 2.275 9.972 0.031 9.867 13.661 20.045 2.672 0.001 45.964 3.772 
Delta Methylmercury TMDL Report J-4 April 2010 

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Delta Methylmercury TMDL Report K-1 April 2010 

K. FISH MERCURY CONCENTRATION DATA INCORPORATED IN TMDL REPORT 

Regional Board staff compiled and evaluated mercury concentration results for more than 

2,800 fish samples collected from Delta waterways between 1970 and 2002. Because of the 

extensive nature of the raw data, a paper copy of the data set is not included in this report. 

Instead the database is available electronically in a Microsoft Excel file upon request or from the 

following website: 

http://www.waterboards.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/delta_hg/ 

The database includes sample results from the following sources: 

CDFG. 1973. Department of Fish and Game Striped Bass Mercury Data, 1970-1973. 

Davis, J.A, B.K. Greenfield, G. Ichikawa and M. Stephenson. 2003. Mercury in Sport Fish from 

the Delta Region. Final report submitted to the CALFED Bay-Delta Program for the project: 

An Assessment of the Ecological and Human Health Impacts of Mercury in the Bay-Delta 

Watershed (Task 2A). San Francisco Estuary Institute and Moss Landing Marine 

Laboratories. Available at: http://loer.tamug.tamu.edu/calfed/FinalReports.htm. 

Davis, J.A., M.D. May, G. Ichikawa, and D. Crane. 2000. Contaminant Concentrations in Fish 

from the Sacramento-San Joaquin Delta and Lower San Joaquin River – 1998. San 

Francisco Estuary Institute report. Richmond, California. September 2000. Available at: 

http://www.sfei.org/sfeireports.htm. 

ICEM. 1971. Mercury in the California Environment. Compiled by the Interagency Committee 

on Environmental Mercury, July 1970 - July 1971. Published by the California State 

Department of Public Health, Environmental Health and Consumer Protection Program. 

Berkeley, California. 

LWA. 2003. Sacramento River Watershed Program Annual Monitoring Report: 2001–2002 

(Final Draft). Larry Walker and Associates (LWA). Davis, CA. June 2003. Available at: 

http://www.sacriver.org/. 

Schwarzbach, S. and T. Adelsbach. 2002. Field Assessment of Avian Mercury Exposure in the 

Bay-Delta Ecosystem. Submitted to the CALFED Bay-Delta Program for the project: An 

Assessment of the Ecological and Human Health Impacts of Mercury in the Bay-Delta 

Watershed (Task 3A). U.S. Geological Survey Biological Research Division and U.S. Fish 

and Wildlife Service. September 2002. Available at: 

http://loer.tamug.tamu.edu/calfed/FinalReports.htm. 

SWRCB-DWQ. 2002. State Mussel Watch Program / Toxic Substances Monitoring Program. 

Electronic databases. State Water Resources Control Board, Division of Water Quality 

(SWRCB-DWQ). Available at: http://www.waterboards.ca.gov/programs/smw/. 

Slotton, D.G., S.M. Ayers, T.H. Suchanek, R.D. Weyland, A.M. Liston, C. Asher, D.C. Nelson, 

and B. Johnson. 2002. The Effects of Wetland Restoration on the Production and 

Bioaccumulation of Methylmercury in the Sacramento-San Joaquin Delta, California. Draft 

final report submitted to the CALFED Bay-Delta Program for the project: An Assessment of 

the Ecological and Human Health Impacts of Mercury in the Bay-Delta Watershed. 

University of California, Davis, Dept. of Environmental Science and Policy, Dept. of Wildlife, 

Fish & Conservation Biology, and Division of Microbiology; U.S. Fish and Wildlife Service, 

Division of Environmental Contaminants. Available at: 

http://loer.tamug.tamu.edu/calfed/DraftReports.htm. 
Delta Methylmercury TMDL Report K-2 April 2010 

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Delta Methylmercury TMDL Report L-1 April 2010 

L. AQUEOUS METHYLMERCURY, TOTAL MERCURY AND TSS CONCENTRATION DATA 

INCORPORATED IN TMDL REPORT 

Central Valley Water Board staff compiled and evaluated methylmercury, total mercury, and 

TSS concentration results for thousands of water and effluent samples characterizing Delta 

inputs and exports. Because of the extensive nature of the raw data, a paper copy of the data 

set is not included in this report. Instead the database is available electronically in a Microsoft 

Excel file upon request or from the following website: 

http://www.waterboards.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/delta_hg/ 

The database includes sample results from ongoing Central Valley Water Board sampling 

programs, NPDES facility and MS4 monitoring reports, and the following sources: 

Alpers, C.N., R.C. Antweiler, H.E. Taylor, P.D. Dileanis, and J.L. Domagalski, 2000. Metals 

Transport in the Sacramento River, California, 1996-1997, Volume1: Methods and Data. 

U.S. Geological Survey Water-Resources Investigation Report 99-4286. Sacramento, CA. 

CMP. 2004. Microsoft Access database of Coordinated Monitoring Program water quality data 

through August 2003. Database and updates provided by Larry Walker Associates (Mike 

Trouchon) and Sacramento Regional County Sanitation District (Steve Nebozuk, CMP 

Program Manager) to Central Valley Regional Water Quality Control Board (Michelle Wood, 

Environmental Scientist, Sacramento). 

Domagalski J, Slotton DG, Alpers CN, Suchanek TH, Churchill RK, Bloom NS, Ayers SM, 

Clinkenbeard JP, 2002. Summary and Synthesis of Mercury Studies in the Cache Creek 

Watershed, California, 2000-2001. Final Report. U.S. Geological Survey; UC Davis; U.S. 

Fish and Wildlife Service; California Department of Conservation; California Geological 

Survey; and Frontier Geosciences, Inc. Prepared for the CALFED Bay-Delta Program, 

Directed Action #99-B06. Available at: http://loer.tamug.tamu.edu/calfed/FinalReports.htm. 

Domagalski, J.L., P.D. Dileanis, D.L. Knifong, C.M. Munday, J.T. May, B.J. Dawson, J.L. 

Shelton, and C.N. Alpers. 2000. Water-Quality Assessment of the Sacramento River Basin, 

California: Water-Quality, Sediment and Tissue Chemistry, and Biological Data, 1995-1998. 

U.S. Geological Survey Open-File Report 00-391. Available at: 

http://ca.water.usgs.gov/sac_nawqa/waterindex.html 

DWR. 2001. California Department of Water Resources Special Tributary Project and Offstream 

Storage Investigation (OSI). Unpublished electronic data e-mailed by DWR (Jerry Boles) to 

Central Valley Regional Water Quality Control Board (Michelle Wood, Environmental 

Scientist, Sacramento) on October 15, 2001. 

Foe, C.G. 2003. Mercury Mass Balance for the Freshwater Sacramento-San Joaquin Bay-Delta 

Estuary. Final report submitted to the CALFED Bay-Delta Program for the project: An 

Assessment of the Ecological and Human Health Impacts of Mercury in the Bay-Delta 

Watershed (Task 1A). California Regional Water Quality Control Board, Central Valley 

Region. Sacramento, CA. Available at: http://loer.tamug.tamu.edu/calfed/FinalReports.htm. 

Foe, C.G. and W. Croyle. 1998. Mercury Concentrations and Loads from the Sacramento River 

and from Cache Creek to the Sacramento-San Joaquin Delta Estuary. California Regional 

Water Quality Control Board, Central Valley Region. Sacramento, CA. Staff report. 

June 1998. 
Delta Methylmercury TMDL Report L-2 April 2010 

Jones, R. 2002. Unpublished mercury concentration data for Morrison Creek and Laguna Creek 

provided by Roger Jones (Wildlife Biologist, Sacramento Regional County Sanitation 

District Bufferlands, Sacramento County) to Michelle Wood (Environmental Scientist, 

Central Valley Water Board) in an emailed Excel file on 22 March 2002. 

NADP. 2004. National Atmospheric Deposition Program (NRSP-3). NADP Program Office, 

Illinois State Water Survey, 2204 Griffith Dr., Champaign, IL 61820. Mercury Deposition 

Network available at: http://nadp.sws.uiuc.edu/mdn/. 

Slotton, D.G., S.M. Ayers, T.H. Suchanek, R.D. Weyland, A.M. Liston, C. Asher, D.C. Nelson, 

and B. Johnson. 2002. The Effects of Wetland Restoration on the Production and 

Bioaccumulation of Methylmercury in the Sacramento-San Joaquin Delta, California. Draft 

final report submitted to the CALFED Bay-Delta Program for the project: An Assessment of 

the Ecological and Human Health Impacts of Mercury in the Bay-Delta Watershed. 

University of California, Davis, Dept. of Environmental Science and Policy, Dept. of Wildlife, 

Fish & Conservation Biology, and Division of Microbiology; U.S. Fish and Wildlife Service, 

Division of Environmental Contaminants. Available at: 

http://loer.tamug.tamu.edu/calfed/DraftReports.htm. 

SRWP. 2004. Microsoft Access database that compiles Sacramento River Watershed water 

quality data collected for the Sacramento River Watershed Program. Database provided by 

Larry Walker Associates (Claus Suverkropp) to Central Valley Regional Water Quality 

Control Board (Michelle Wood, Environmental Scientist, Sacramento). 

Stephenson, M., B. Sohst and S. Mundell. 2002. Mercury Lagrangian Study Between Colusa 

and Hamilton City. Study Conducted by Moss Landing Marine Labs and California 

Department of Fish and Game for the Sacramento Regional County Sanitation District. 

January 2002. 

USGS. 2003. Microsoft Excel Spreadsheets of unpublished data for Bear River Mercury Cycling 

Project. Data provided by USGS (Charlie Alpers, Research Chemist) to Central Valley 

Regional Water Quality Control Board (Michelle Wood, Environmental Scientist, 

Sacramento).