U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2020–1086

Impacts of Periodic Dredging on Macroinvertebrate 

Prey Availability for Benthic Foraging Fishes in Central 

San Francisco Bay, California
Cover Photo: Dredge operating in a shallow subtidal region of San Francisco Bay, California. 

Photo by Hannah Mittelstaedt, U.S. Geological Survey, May 4, 2017.
Impacts of Periodic Dredging on 

Macroinvertebrate Prey Availability for 

Benthic Foraging Fishes in Central San 

Francisco Bay, California

By Susan E. W. De La Cruz, Isa Woo, Laurie Hall, Alison Flanagan, and 

Hannah Mittelstaedt

Open-File Report 2020–1086

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DAVID BERNHARDT, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2020

For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, 

natural hazards, and the environment—visit https://www.usgs.gov or call 1–888–ASK–USGS.

For an overview of USGS information products, including maps, imagery, and publications, visit 

https://store.usgs.gov/.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the 

U.S. Government.

Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials 

as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

De La Cruz, S.E.W., Woo, I., Hall, L., Flanagan, A., and Mittelstaedt, H., 2020, Impacts of periodic dredging on 

macroinvertebrate prey availability for benthic foraging fishes in central San Francisco Bay, California: U.S. Geological 

Survey Open-File Report 2020–1086, 96 p., https://doi.org/10.3133/ofr20201086.

ISSN 2331-1258 (online)
iii

Acknowledgments

Full implementation (Phase IV) of this study was funded by the U.S. Army Corps of Engineers 

(USACE), whereas earlier pilot and study plan development (Phases I–III) were funded by the 

San Francisco Estuary Institute (SFEI) Regional Monitoring Program and the Port of Oakland. 

The study was recommended by the National Marine Fisheries Service through the Long-Term 

Management Strategy (LTMS) Programmatic Consultation on Essential Fish Habitat and the 

San Francisco Bay LTMS for the Placement of Dredged Sediment in the Bay Region, including 

the USACE, U.S. Environmental Protection Agency, San Francisco Bay Conservation and 

Development Commission, and San Francisco Bay Regional Water Quality Control Board.

We thank J. A. Hobbs, S. Hamilton, and F. Feyrer for fisheries consultations, J. Yee 

(U.S. Geological Survey, USGS) for statistical guidance, and J. Donald, Y. Chan, C. Garcia, 

A. Ravani, C. Norton, D. Nelson, M. Hill, M. Tzen, S. Morris, C. Tolle, C. Birdsall, D. Turner, 

G. Bongey, S. Meyers, and R. Babuka for laboratory and field assistance. T. Graham (USGS), 

J. Adams (USGS), A. Loveland (San Francisco Public Utilities Commission), Bay Planning 

Coalition, and the SFEI Regional Monitoring Program Exposure and Effects Workgroup provided 

helpful review comments that improved the overall clarity of this report.

v

Contents

Acknowledgments........................................................................................................................................iii

Background.....................................................................................................................................................1

Introduction.....................................................................................................................................................2

Fish Foraging Ecology ..........................................................................................................................2

Macroinvertebrate Prey Availability ..................................................................................................4

Assessing Benthic Recovery After Maintenance Dredging .........................................................5

Measuring Structural and Functional Recovery ....................................................................6

Methods...........................................................................................................................................................6

Study Design..........................................................................................................................................6

Modified Benthic Resources Assessment Technique (MBRAT) Framework ....................6

Study Area and Site Selection .................................................................................................10

Power Analyses .........................................................................................................................15

Sampling Design ........................................................................................................................17

Sample Processing .............................................................................................................................18

Sample Collection ......................................................................................................................18

Macroinvertebrate Density, Biomass, and Energy Estimations .........................................20

Statistical Analyses ...................................................................................................................21

Results ...........................................................................................................................................................26

Salinity, Elevation, and Sediment Characteristics Among Sites .................................................26

Within-Site Macroinvertebrate Community Composition, Density, Biomass, and 

Energy Content ......................................................................................................................35

Dredged in 2013 ..........................................................................................................................35

Dredged in 2014 ..........................................................................................................................40

Dredged in 2015 ..........................................................................................................................40

The Effect of Dredging on Macroinvertebrate Density, Biomass, and Energy Content ..........45

The Effect of Distance and Time on Macroinvertebrate Density, Biomass and 

Energy Content ......................................................................................................................63

Discussion.....................................................................................................................................................71

Influence of Physical Characteristics .............................................................................................71

The Effect of Dredging on Trophic Support for Target Fishes .....................................................72

The of Effects of Distance and Time ................................................................................................73

Summary........................................................................................................................................................74

References Cited..........................................................................................................................................75

Appendix........................................................................................................................................................85
vi

Figures

1. Diagram showing the Benthic Resource Assessment Technique outlines the 

activities to relate the resource value of benthic macroinvertebrates to fish 

predators ........................................................................................................................................7

2. Graph showing mean density of benthic macroinvertebrates by 2-centimeter 

depth increments at dredged and undredged reference areas sampled at 

Mooring Road and Pier 32 sites during the pilot study ...........................................................9

3. Conceptual diagram illustrating differences in prey consumption for focal 

foraging fish species, and between juvenile and adult fish ................................................10

4. Map of study sites in central San Francisco Bay ..................................................................11

5. Map of sampling locations in the Dumbarton Shoals mudflat adjacent to pond 

RSF2 in the Ravenswood complex of the South Bay Salt Pond Restoration Project ......12

6. Map of San Francisco Bay benthic assemblages .................................................................14

7. Image showing Paradise Cay Homeowners Association study site composed of 

residential docks and berths in western San Francisco Bay ..............................................16

8. Image showing Strawberry Channel study site composed of residential docks 

and berths in dredged channel through residential area and Aramburu Island in 

Richardson Bay ...........................................................................................................................17

9. Image showing Richardson Bay Marina study site composed of marina docks 

and an undredged reference area northeast of the marina ................................................18

10. Image showing Port of San Francisco Pier 32 study site composed of an area 

between piers 32 and 36 in San Francisco .............................................................................19

11. Image showing Mooring Road study site composed of dredged areas around 

residential docks in tidally influenced San Rafael Creek .....................................................20

12. Image showing Loch Lomond Marina study site composed of a marina and 

entrance channel in San Rafael Bay sampled as part of the full study .............................21

13. Image showing Paradise Cay Yacht Harbor study site composed of a marina 

and entrance channel in western San Francisco Bay .........................................................22

14. Graphs showing power analysis curves for individual taxa groups based on the 

comprehensive U.S. Geological Survey Dumbarton macroinvertebrate dataset ............24

15. Graphs showing power analysis curves for individual taxa groups based on the 

2015 pilot study macroinvertebrate dataset ...........................................................................25

16. Bar graph showing summer and winter demersal salinity at six coring sites 

during four sampling periods ....................................................................................................27

17. Bar graph showing elevation in dredged and undredged areas at six study sites .........28

18. Bar graph showing sediment organic matter content measured as percent loss 

on ignition in shallow and deep cores of dredged and undredged areas at six 

study sites in San Francisco Bay .............................................................................................29

19. Bar graph showing percent silt in sediments from shallow and deep cores of 

dredged and undredged areas at six study sites in San Francisco Bay ...........................30

20. Bar graphs showing percent sand in sediments from shallow and deep cores 

of dredged and undredged areas at six study sites in San Francisco Bay .......................31

21. Bar graph showing percent clay in sediments from shallow and deep cores of 

dredged and undredged areas at six study sites in San Francisco Bay ...........................32

22. Bar graph showing sediment pH measured in shallow and deep cores of 

dredged and undredged areas at six study sites in San Francisco Bay ...........................33
vii

23. Sediment triangles used to classify sediment texture with percent sand, 

percent silt, and percent clay from sediments collected in dredged and 

undredged areas at six study sites in San Francisco Bay ...................................................34

24. Graph showing mean densities of macroinvertebrate taxa in dredged and 

undredged areas at seven sites in San Francisco Bay ........................................................41

25. Graph showing mean biomass of macroinvertebrate taxa in dredged and 

undredged areas at six sites in San Francisco Bay ..............................................................42

26. Graph showing mean energy of macroinvertebrate taxa in dredged and 

undredged areas at six sites in San Francisco Bay ..............................................................43

27. Graph showing mean densities of macroinvertebrate taxa collected in dredged 

and undredged areas at five pilot study sites in November 2015 .......................................46

28. Graph showing mean densities of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in August 2016 .......................................................47

29. Graph showing mean densities of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in January 2017 .....................................................48

30. Graph showing mean densities of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in August 2017 .......................................................49

31. Graph showing mean density of macroinvertebrate taxa from different size 

classes in shallow cores from dredged and undredged areas at six study sites 

in San Francisco Bay .................................................................................................................50

32. Graph showing mean density of macroinvertebrate taxa from different size 

classes in deep cores from dredged and undredged areas at six study sites in 

San Francisco Bay ......................................................................................................................51

33. Graph showing mean biomass of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in August 2016 .......................................................52

34. Graph showing mean biomass of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in January 2017 .....................................................53

35. Graph showing mean biomass of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in August 2017 .......................................................54

36. Graph showing mean biomass of macroinvertebrate taxa from different size 

classes in shallow cores from dredged and undredged areas at six study sites 

in San Francisco Bay .................................................................................................................55

37. Graph showing mean biomass of macroinvertebrate taxa from different size 

classes in deep cores from dredged and undredged areas at six study sites in 

San Francisco Bay ......................................................................................................................56

38. Graph showing mean energy of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in August 2016 .......................................................58

39. Graph showing mean energy of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in January 2017 .....................................................59

40. Graph showing mean energy of macroinvertebrate taxa collected in dredged 

and undredged areas at six study sites in August 2017 .......................................................60

41. Graph showing mean energy of macroinvertebrate taxa from different size 

classes in shallow cores from dredged and undredged areas at six study sites 

in San Francisco Bay .................................................................................................................61

42. Graph showing mean energy of macroinvertebrate taxa from different size 

classes in deep cores from dredged and undredged areas at six study sites in 

San Francisco Bay ......................................................................................................................62

43. Graph showing change in macroinvertebrate density by size class in shallow 

and whole core fractions with increasing distance from a dredged area .......................64
viii

44. Graph showing change in macroinvertebrate biomass by size class in shallow 

and whole core fractions with increasing distance from a dredged area .......................65

45. Graph showing change in macroinvertebrate energy by size class in shallow 

and whole core fractions with increasing distance from a dredged area .......................67

46. Graph showing change in macroinvertebrate density by size class in shallow 

and whole core fractions with increasing time since a site was dredged .......................68

47. Graph showing change in macroinvertebrate biomass by size class in shallow 

and whole core fractions with increasing time since a site was dredged .......................69

48. Graph showing change in macroinvertebrate energy by size class in shallow 

and whole core fractions with increasing time since a site was dredged .......................70

Tables

1. Foraging depth, common macroinvertebrate prey, foraging mode, and prey size 

class for focal fish species juveniles and adults .....................................................................3

2. Simplified foraging table for focal fish species showing the depth increments 

and prey class sizes used in the MBRAT assessment ...........................................................8

3. Central Bay site selection table indicating all sites considered for the pilot and 

full study .......................................................................................................................................13

4. Sampling scenarios used in simulation power analyses to determine project 

sample size ..................................................................................................................................23

5. GLM results for demersal salinity as a function of site and sampling period ..................26

6. GLM results for core elevation as a function of site .............................................................26

7. Macroinvertebrate taxa identified in shallow cores from dredged and 

undredged locations at six sites in San Francisco Bay, California ....................................36

8. Macroinvertebrate taxa identified in deep cores from dredged and undredged 

locations at six sites in San Francisco Bay, California .........................................................39

9. Comparison of mean macroinvertebrate density, biomass in dry weight, and 

energy in dredged and undredged areas during the pilot and full study in each site ....44

10. Summary of GLMM results for total density of macroinvertebrates from 

different size classes found in shallow and deep cores at six sites with dredged 

and undredged areas .................................................................................................................45

11. Summary of GLMM results for total biomass of macroinvertebrates from 

different size classes found in shallow and deep cores at six sites within 

dredged and undredged areas .................................................................................................45

12. Summary of GLMM results for total energy of macroinvertebrates from 

different size classes found in shallow and deep cores at six sites within 

dredged and undredged areas .................................................................................................57

13. Summary of GLMM results testing the effects of distance from dredged areas, 

season, salinity, and elevation on total density of macroinvertebrates from 

different size classes found in shallow and deep cores at six sites ..................................63

14. Summary of GLMM results testing the effects of distance to nearest dredged 

areas, season, salinity, and elevation on total biomass of macroinvertebrates 

from different size classes found in shallow and deep cores at six sites .........................63

15. Summary of GLMM results testing the effects of distance from dredged areas, 

season, salinity, and elevation on total energy of macroinvertebrates from 

different size classes found in shallow and deep cores at six sites ..................................66
ix

16. Summary of GLMM results testing the effects of time-since-dredged, season, 

salinity, and elevation on total density of macroinvertebrates from different size 

classes found in shallow and deep cores at six sites ..........................................................66

17. Summary of GLMM results testing the effects of time since dredged, season, 

salinity, and elevation on total biomass of macroinvertebrates from different 

size classes found in shallow and deep cores at six sites ..................................................66

18. Summary of GLMM results testing the effects of time since dredged, season, 

salinity, and elevation on total energy of macroinvertebrates from different size 

classes found in shallow and deep cores at six sites ..........................................................66

Conversion Factors

International System of Units to U.S. customary units

Multiply By To obtain

Length

micrometer (μm) 0.0004279515 inch (in)

centimeter (cm) 0.3937 inch (in)

millimeter (mm) 0.03937 inch (in)

meter (m) 3.281 foot (ft)

kilometer (km) 0.6214 mile (mi)

kilometer (km) 0.5400 mile, nautical (nmi)

meter (m) 1.094 yard (yd)

Area

square meter (m2) 0.0002471 acre

square kilometer (km2) 247.1 acre

square meter (m2) 10.76 square foot (ft2)

square kilometer (km2) 0.3861 square mile (mi2)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

Energy

joule (J) 0.2388459 calorie (cal)

kilojoules (kJ) 238.8459 Calorie (cal)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F = (1.8 × °C) + 32.

Datum

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Elevation, as used in this report, refers to distance above the vertical datum.
x

Abbreviations

AFDM ash-free dry mass

AIC Akaike’s Information Criterion

BACI Before After Control Impact

BRAT Benthic Resources Assessment Technique

°C degree Celsius

dw dry weight

EFH Essential Fish Habitat

EPA Environmental Protection Agency

ESA Endangered Species Act

FMP Fishery Management Plan

GLM General Linear Models

GLMM Generalized Linear Mixed Models

HEP Habitat Evaluation Program

HOA Homeowners Association

LDF Linear Discriminant Function

LTMS Long Term Management Strategy

MBRAT Modified Benthic Resources Assessment Technique

MLLW mean lower low water

MSA Magnuson-Stevens Fishery Conservation and Management Act

NMFS National Marine Fisheries Service

ppt parts per thousand

psu practical salinity units

SFB San Francisco Bay

SFRWQCB San Francisco Regional Water Quality Control Board

U.S.A. United States of America

USACE U.S. Army Corps of Engineers

USFWS U.S. Fish and Wildlife Service

USGS U.S. Geological Survey
Impacts of Periodic Dredging on Macroinvertebrate 

Prey Availability for Benthic Foraging Fishes in Central 

San Francisco Bay, California

By Susan E.W. De La Cruz,1 Isa Woo,1 Laurie Hall,1 Alison Flanagan,1, 2 and Hannah Mittelstaedt1, 3

Background

Because of its importance for species covered under 

Federal Fishery Management Plans (FMPs), the San 

Francisco Bay (SFB) estuary has been designated as Essential 

Fish Habitat (EFH) under the Magnuson-Stevens Fishery 

Conservation and Management Act (MSA; 16 United 

States Code §18559b). Within this estuary, benthic 

macroinvertebrate communities provide important prey 

resources for many economically significant fish species 

that rely on EFH. Periodic maintenance dredging can impact 

benthic communities; however, there is a lack of scientific 

information specific to SFB regarding dredging effects on 

macroinvertebrates in fish foraging areas. In addition, rates 

of benthic community recolonization and recovery following 

dredging and subsequent effects on foraging fish are unknown. 

For this reason, it is difficult for regulatory and resource 

agencies to determine the impacts of maintenance dredging. 

Thus, the National Marine Fisheries Service (NMFS) and 

the consortium of agencies (U.S. Environmental Protection 

Agency [EPA], U.S. Army Corp of Engineers [USACE], 

San Francisco Regional Water Quality Control Board 

[SFRWQCB], and San Francisco Bay Conservation and 

Development Commission [BCDC]) that make up the San 

Francisco Bay Long Term Management Strategy for Dredging 

(LTMS) identified a study of dredging impacts on SFB fish 

foraging habitat as one of their highest priorities in their 2011 

Programmatic EFH Agreement (U.S. Army Corp of Engineers 

and U.S. Environmental Protection Agency, 2011).

The LTMS agencies identified the region of interest as 

shallow (<13 feet [<4 meters (m)] mean lower low water 

[MLLW]), soft-bottom (silt/clay soil texture) areas in the 

Central Bay of SFB that were periodically dredged (every 

1–3 years). Fish species of interest were compiled by NMFS 

and included those managed by the Pacific Groundfish, Pacific 

Salmon, and Coastal Pelagic FMPs (pursuant to the MSA) 

as well as those listed under the California State or Federal 

Endangered Species Act (ESA; 16 U.S.C. §1531–1544) as 

threatened or endangered. Target species included leopard 

shark (Triakis semifasciata), big skate (Raja binoculata), 

English sole (Parophrys vetulus), starry flounder 

(Platichthys stellatus), brown rockfish (Sebastes auriculatus), 

green sturgeon (Acipenser medirostris; threatened species 

under Federal ESA), northern anchovy (Engraulis mordax), 

longfin smelt (Spirinchus thaleichthys, threatened under 

California ESA), and Pacific sardine (Sardinops sagax). 

In addition, Dungeness crab (Cancer magister), California 

halibut (Paralichthys californicus), and white sturgeon 

(Acipenser transmontanus) also were included because they 

are substantial contributors to the California State fishery.

To address LTMS priorities, U.S. Geological Survey, 

Western Ecological Research Center, San Francisco Bay 

Estuary Field Station (hereafter USGS) conducted a 

multi-phased project including an initial literature review, 

study design, pilot study, and implementation of a full study. 

The overarching goal was to assess the effects of periodic 

dredge operations (every 1–3 years) on benthic habitat 

for foraging fish in the Central Bay, with emphasis on the 

foraging requirements of target fish species and analyses of 

benthic macroinvertebrates in dredged areas compared to 

adjacent undredged reference areas. The USGS partnered 

with University of California, Davis, fisheries expert James 

Hobbs to synthesize existing knowledge of fish foraging 

ecology and review benthic infauna community composition 

in SFB with a focus on the Central Bay. The literature 

review (Phase I; De La Cruz and others, 2016) addressed key 

questions identified by the LTMS on benthic foraging fish in 

the study area, including the following: (1) What are target 

fish eating? (2) What are the seasonal differences in prey items 

and macroinvertebrate assemblages? (3) What are the annual 

differences in prey items and macroinvertebrate assemblages? 

(4) What are the predominant macroinvertebrate functional 

groups from the perspective of fish foraging? Phase II 

consisted of creating a framework for a functional assessment 

of maintenance dredging effects on foraging fish and drafting 

a full study design (De La Cruz and others, 2017), which 

was then tested in the Phase III pilot study. The Phase IV full 

study incorporated lessons learned from the pilot study. Here 

we focus on the results of the full study and implications for 

benthic foraging fishes.

1U.S. Geological Survey.

2San Diego Zoo Global.

3University of Maine.
2 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Introduction

San Francisco Bay, the largest estuary on the Pacific 

coast of North America, has been greatly modified by human 

development for commercial, residential, and recreational 

purposes (Nichols and others, 1986; Cohen and Carlton, 

1998). Despite this urban estuary’s extensive history of habitat 

alteration, SFB remains home to myriad wildlife and continues 

to provide essential ecosystem functions through its role as a 

nursery, maturation area, and foraging habitat for many fishes 

including several state and Federal ESA-listed species (for 

example, longfin smelt, winter and spring-run Chinook salmon 

[Oncorhynchus tshawytscha], and green sturgeon) and species 

of economic importance (Dungeness crab, California halibut, 

and white sturgeon). Furthermore, SFB has been designated 

as EFH in the Pacific Groundfish, Pacific Salmon, and Coastal 

Pelagic FMPs pursuant to the MSA.

In urbanized estuaries, dredging (the action of removing 

benthic sediment) is often necessary at varying intervals 

and intensities to maintain access to shallow-water facilities 

such as marinas, harbors, and navigational channels. Though 

periodic and recurring dredge activities may be necessary 

to maintain waterway access, the impacts of maintenance 

dredging on fish habitat are largely unknown. Dredging is 

a localized disturbance that can adversely impact benthic 

communities either directly by the removal of organisms 

(via mortality or injury by entrainment, impingement, or 

burial; Hirsch and others, 1978; Nightingale and Simenstad, 

2001) or indirectly by reducing habitat quality (for example, 

releasing buried organic matter, nutrients, or contaminants, 

and increasing suspended sediment concentrations; Reilly 

and others, 1992; Newell and others, 1998; Ray, 2005). 

Maintenance dredging may also indirectly impact benthic 

communities by increasing predation risk and (or) facilitating 

the colonization of opportunistic non-native or invasive 

species (Hanson and others, 2004). These physical changes 

can have cascading impacts on benthic communities (for 

example, altered composition and species abundance) and 

subsequently on fishes that forage on benthic infauna (Hirsch 

and others, 1978; LaSalle, 1990; Clarke and others, 2000; 

Dernie and others, 2003; Lebednik, 2004; Ray and others, 

2005; Rich, 2010).

Fish Foraging Ecology

Shallow subtidal and intertidal benthos are key foraging 

areas for many fish species. Knowledge of fish diets and prey 

accessibility (including, prey burial depth, prey size class) 

are fundamental to understanding the foraging value of the 

benthos for demersal fishes. Specific data about diets and prey 

sizes of fishes are generally lacking for SFB (De La Cruz and 

others, 2016), and much of the limited existing information 

on macroinvertebrate prey is at a broad taxonomic level (for 

example, crustaceans). Many of the target fish species for 

this study are considered generalist foragers that consume 

a wide variety of organisms depending on species-specific 

physiological constraints (such as, gape size, maximum 

foraging depth) and life history traits that can often change 

from juvenile to adult life (ontogenic) stages (De La Cruz 

and others, 2016; table 1). For example, leopard sharks and 

big skates are opportunistic generalists known to forage on 

benthic macroinvertebrates (such as, crabs, molluscs, shrimp, 

polychaetes), and as they grow, they tend to consume other 

fish (Hart, 1973; Talent, 1976; Motta and Wilga, 2001; Ebert 

and Ebert, 2005; Yang, 2007). Whereas juvenile green and 

white sturgeon consume opossum shrimp and amphipods 

(Radtke, 1966; Muir and others, 1988), adults consume 

a wider range of macroinvertebrates and fishes (Adams 

and others, 2002). Within estuaries, smaller California 

halibut use shallow habitats and have a predominantly 

macroinvertebrate-based diet but switch to a more fish-based 

diet as they grow and inhabit deeper channels (Allen, 1988). 

Pelagic fishes, including northern anchovy and Pacific sardine, 

exhibit two distinct modes of feeding: particulate feeding 

(individual prey items are attacked and consumed) and 

filter feeding (small food particles are collected and strained 

through the fine filaments in the gill rakers; Blaxter and 

Hunter, 1982). In some species, adults will actively switch 

between particulate and filter feeding modes depending on 

prey availability. Larval and young juvenile smelt primarily 

feed on calanoid copepods, including Eurytemora affinis

(Baxter and others, 1999) and other crustaceans, and mature 

juveniles and adult fish feed predominantly on opossum 

shrimp (Neomysis mercedis, Acanthomysis sp.) and copepods 

(Feyrer and others, 2003; Hobbs and others, 2006).

The relative abundance of adult and juvenile fish in the 

Central Bay varies seasonally and by species (De La Cruz 

and others, 2016). For instance, juvenile northern anchovy 

are present year-round, but adults are absent during winter. 

Juvenile Pacific herring (Clupea pallasii) are abundant 

throughout SFB in spring and summer, whereas adult herring 

are more abundant in winter when they spawn on substrates 

such as eelgrass and wharf pilings (Skinner, 1962). California 

halibut of varying age classes are abundant throughout 

winter, spring, early summer, and fall, with fewer individuals 

collected in mid-summer months (California Department 

of Fish and Wildlife, 2013). Young leopard sharks are 

abundant year-round in SFB and spend many years maturing 

in SFB before migrating offshore to reproduce (Ebert and 

Ebert, 2005).

The foraging value of the shallow benthos for generalist 

fishes can be evaluated using the metric of prey profitability, 

which compares the energy gained to the energy expended 

to capture and ingest prey. Prey profitability has been used 

to evaluate habitat quality and carrying capacity for many 

benthic foraging predators (Godin and Keenleyside, 1984). 

The energy content and accessibility (prey size in relation to 

fish gape size, and the vertical distribution in the sediment) 

of macroinvertebrates are integral to determining their 

availability to benthic foraging fishes (Piet and others, 1998; 

van Denderen and others, 2013).
Introduction 3

Table 1. Foraging depth, common macroinvertebrate prey, foraging mode, and prey size class for focal fish species juveniles 

and adults.

[Information was obtained during the Phase I Literature Review and from local expert opinion1. Abbreviaitons: mm, millimeter; <, less than; cm, centimeter]

Fish 

species

Life 

stage Common prey taxa Foraging mode

Maximum 

prey size 

class

(mm)

References

Foraging depth: shallow (0–4 cm)

Pacific 

sardine

Juvenile Euphausids, copepods, diatoms, 

Oikopluera spp., fish eggs

Picker, filter1 4 Emmett and others, 2005; McFarlane and 

others, 2010

Adult Phytoplankton, copepods, euphasids, 

diatoms, pelagic fish eggs

Particle, filter1 24 Munuera Fernandez and Gonzalez-Quiros, 

2006; Espinoza and others, 2009

Longfin 

smelt

Juvenile Copepods (e.g. Eurytemora affinis), 

crustaceans

Picker1 4 Moyle and Davis, 2000; Hobbs and others, 

2006; Baxter, 2009

Adult Mysid shrimp, copepods, 

zooplankton, crustaceans

Picker1 24 Boubee and Ward, 1997; Chigbu and others, 

1998; Feyrer and others, 2003; Hobbs and 

others, 2006

Northern 

anchovy

Juvenile Copepod nauplii, phytoplankton Filter 

(particulates)1

4 Hunter, 1977; Parrish and others, 1985; 

Miller and Brodeur, 2007

Adult small crustaceans, copepods, 

phytoplankton

Filter 

(particulates)

100 Leong and O’Connell, 1969; Longhurst, 

1971; Blaxter and Hunter, 1982; Miller 

and Brodeur, 2007

English 

sole

Juvenile Polychaetes, bivalves, amphipods, 

cumaceans, copepods

Picker1 12 Ambrose, 1976; Toole, 1980; Hogue and 

Carey, Jr., 1982; Gadomski and Boehlert, 

1984; Lassuy, 1989

Adult Gammarid amphipods (summer), 

polychaetes (fall)

Picker1 50 Ambrose, 1976; Buechner and others, 1981; 

Clarke, 1986

Starry 

flounder

Juvenile Mysid shrimp, copepods, amphipods, 

insect larvae (in freshwater)

Picker1 12 Ambrose, 1976; Moore and Moore, 1976; 

McCall, 1992; Moyle and Davis, 2000

Adult Crabs, polychaetes, molluscs, 

amphipods, isopods, copepods, 

mysid shrimp

Picker1 100 Orcutt, 1950; Miller, 1967; Ambrose, 1976; 

Moore and Moore, 1976; Herbold, 1987

Brown 

rockfish

Juvenile Crustaceans, amphipods, isopods, 

eelgrass epifauna

Picker1 Unknown Bizzarro and others, 2017; Love and others, 

2002

Adult Fish Picker1 100 Washington and others, 1978

California 

halibut

Juvenile Caridean shrimp, crabs, small fishes Ambush1 50 Allen, 1988; Madon, 2002

Adult Fish Visual, ambush1 100 Allen, 1988; Haugen, 1990

Foraging depth: deep (0–10 cm)

Dungeness 

crab

Juvenile Clams, crustaceans, fish Opportunistic, 

scavenger, 

grazer1

100 Stevens and others, 1982; Jensen and 

Asplen, 1998

Adult Clams, crustaceans, fish Omnivore, 

opportunistic, 

scavenger, 

grazer1

100 Stevens and others, 1982; Jensen and 

Asplen, 1998

Big skate Juvenile Fish, shrimp, euphausiids Opportunistic 

generalist, 

inertial 

suction

100 Motta and Wilga, 2001; Yang, 2007; 

Bizzarro and others, 2007
4 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 1. Foraging depth, common macroinvertebrate prey, foraging mode, and prey size class for focal fish species juveniles and 

adults.—Continued

[Information was obtained during the Phase I Literature Review and from local expert opinion1. Abbreviaitons: mm, millimeter; <, less than; cm, centimeter]

Fish 

species

Life 

stage Common prey taxa Foraging mode

Maximum 

prey size 

class

(mm)

References

Adult Crabs, cephalopods, demersal 

teleosts, shrimps, polychaetes, 

clams, sculpin, pelagic skate

Opportunistic 

generalist

100 Ackerman, 1971; Russo, 1975; Talent, 1976; 

Kao, 2000; Robinson and others, 2007; 

Yang, 2007; Bizzarro and others, 2007; 

Reecht and others, 2013

Green 

sturgeon

Juvenile Drifting and benthic insects 

(seasonally), oligochaetes, 

amphipods, small fish, fish eggs, 

mysid shrimp

Opportunistic 

generalist1

100 Radtke, 1966; Gessner and others, 2007; 

Dumbauld and others, 2008

Adult Shrimp, molluscs, amphipods, small 

fish

Opportunistic, 

suction

100 Adams and others, 2002; Moyle, 2002; 

Dumbauld and others, 2008

White 

sturgeon

Juvenile Amphipods (e.g. Corophium spp.), 

mysid shrimp

Suction 100 Radtke, 1966; Muir and others, 1988; 

McCabe and others, 1993; Moyle and 

Davis, 2000; Dumbauld and others, 2008; 

Bogacka-Kapusta and others, 2011

Adult Shrimp, crabs, clams, herring, 

anchovy, striped bass, starry 

flounder, smelt, herring eggs

Suction 100 McKechnie and Fenner, 1971; Miller, 2004; 

Dumbauld and others, 2008

Leopard 

shark

Juvenile Crabs (e.g. Hemigrapsus oregonensis) Opportunistic 

generalist, 

disturb mud, 

inertial 

suction

100 Talent, 1976; Barry, 1983; Barry and others, 

1996; Ferry-Graham, 1998; Motta and 

Wilga, 2001

Adult Fishes, crabs, clam siphons, 

innkeeper worms (e.g. Urechis 

caupo), fish eggs (e,g, Atherinopsis 

californiensis), isopods, 

amphipods, zooplankton, shrimp, 

teleosts, small elasmobranch

Opportunistic 

generalist, 

disturb mud, 

inertial 

suction

100 Talent, 1976; Barry, 1983; Barry and others, 

1996; Motta and Wilga, 2001; Stewart and 

others, 2004; Ebert and Ebert, 2005

1Expert opinion, James Hobbs, University of California, Davis.

Macroinvertebrate Prey Availability

Benthic and epibenthic macroinvertebrates are important 

prey resources for fish, birds, and other predators. Benthic 

infauna also form an interface between sediment properties 

and the aquatic food web by facilitating nutrient flux through 

their burrowing and feeding activities within the sediment 

(Nichols and Pamatmat, 1988; Thompson and others, 2000; 

Weigelhofer and Waringer, 2003; Cardoso and others, 2010). 

Benthic macroinvertebrate communities in SFB commonly 

include gastropods, bivalves, polychaetes, oligochaetes, and 

several crustaceans (such as., amphipods, isopods, copepods, 

crabs, mysids and shrimp; Thompson and others, 2007, 2013).

The distribution and community composition of 

benthic infauna is largely controlled by salinity (Nichols 

and Pamatmat, 1988). In winter months, during periods of 

high freshwater input, the surface salinity in the Central Bay 

can rapidly decline from 30 to 10 parts per thousand (ppt); 

however, salinity values in the demersal waters tend to be 

more stable owing to stratification of the less dense surface 

freshwater (Cloern and others, 2000). Because salinity in the 

Central Bay is more stable than in the northern reaches of 

SFB, it sustains a more diverse community across seasons 

(Thompson and others, 2000). Still, large freshwater influx in 

the Central Bay can affect the benthos in shallow shoal areas 

(Thompson and others, 2007).
Introduction 5

Although benthic macroinvertebrate communities 

are most influenced by salinity gradients within SFB, 

macroinvertebrate abundance, taxonomic richness, and spatial 

distributions are also influenced by other physical factors such 

as temperature, flow velocities, and substrate characteristics 

(for example, texture and particle size; Thompson and others, 

2000). In shallow shoals, sediment composition and particle 

size are largely influenced by physical processes such as 

wave action and water flow velocity (Krone, 1979; van 

Duren and Middelburg, 2001). Benthic habitats with greater 

proportions of fine particles such as silt and clay contain 

different macroinvertebrate species than coarser sediments 

such as sand and shell fragments, resulting in distinct benthic 

community assemblages.

Much of the benthic substrate throughout the Central Bay 

consists of a mixture of sand, silt, clay, and shell fragments 

(Goals Project, 1999; California State Coastal Conservancy, 

2010; Barnard and others, 2013; Greene and others, 2013); 

however, the shallow benthic regions that are the focus 

of this study are characterized predominately by muddy, 

fine-grained sediment substrates, which are dominated 

by amphipods (primarily Ampelisca abdita as well as 

Monocorophium acherusicum) and mobile errant polychaetes 

(primarily Euchone limnicola; Thompson and others, 

2000; Lee II and others, 2003). Benthic macroinvertebrate 

density and taxonomic richness are frequently greater in 

these low-flow habitats with fine sediments, whereas sandy 

substrates with swift-moving currents are typically dominated 

by polychaete species (Heteropodarke heteromorpha and 

E. limnicola; Thompson and others, 2000, 2007; Lee II and 

others, 2003).

Assessing Benthic Recovery After 

Maintenance Dredging

In urbanized estuaries, maintenance dredging and 

resulting localized disturbances often occur at regular 

or periodic intervals to maintain access to harbors, 

marinas, and waterways. Benthic recovery post-dredging 

is complicated by the fact that repopulation may occur 

at different rates for different taxa. In general, large, 

hard-bodied macroinvertebrates with greater longevity have 

longer recovery times and are disproportionately affected 

by disturbance. Smaller species are often associated with 

high fecundity and shorter generation times and thus are 

conceivably more resilient to disturbance (McCall, 1977; 

Newell and others, 1998; van Denderen and others, 2013). 

Recolonization is primarily driven by the lateral movement of 

organisms, larval settlement, and appropriate conditions for 

larval settlement and growth. Initial colonizers are generally 

opportunistic species that may differ from those that were 

present prior to sediment removal (Oliver and others, 1977; 

Newell and others, 1998; Applied Marine Sciences Inc., 

2009; Cohen, 2010). Following disturbance, a transitional 

community with lower peak abundances than the initial 

colonizers will appear, but it may take several years for larger 

and longer-lived taxa to recolonize and grow (McCall, 1977; 

Van Der Veer and others, 1985; Rhoads and Germano, 1986; 

Newell and others, 1998). Thus, chronic disturbance may 

change a community of large, hard-bodied macroinvertebrates 

to one that is dominated by smaller, soft-bodied species (such 

as, polychaetes) with low species diversity (Rhoads and 

Germano, 1986; Rees and Dare, 1993; Newell and others, 

1998; van Denderen and others, 2013). On the other hand, 

some studies indicate that with enough time, the re-established 

biotic community might recover and resemble the pre-dredged 

community (Oliver and others, 1977; Newell and others, 1998; 

Applied Marine Sciences Inc., 2009; Cohen, 2010).

Defining benthic recovery remains a major challenge, 

despite the post-dredging impact studies that have been 

conducted over the past several decades. Several methods 

have been suggested for evaluating recovery, but there is 

little consensus concerning the appropriate metrics (such 

as, macroinvertebrate density, biomass, species richness, 

evenness, and diversity) or statistical techniques to assess 

post-disturbance recovery (Rhoads and Germano, 1986; 

Bolam and Rees, 2003; Wilber and Clarke, 2007; Wilber and 

others, 2008). As a result, recovery estimates are variable 

(Bolam and others, 2006; Wilber and Clarke, 2007). Recovery 

is often defined as a return to a baseline (pre-impact) or 

reference (unimpacted) condition and tested for using a 

BACI (Before-After Control-Impact; Currie and Parry, 1996; 

Wilber and others, 2008) or Beyond BACI (an asymmetrical 

BACI design using multiple reference sites to assess impacts; 

Underwood, 1994; Roberts and others, 1998a, 1998b) design. 

The combination of natural and anthropogenic disturbances is 

common in estuaries such that the baseline macroinvertebrate 

community (in other words, pre-dredging) may not be 

representative of a natural, “healthy” community, and 

instead may be dominated by a few small, opportunistic taxa 

commonly found in areas that are frequently or chronically 

disturbed. Newell and others (1998) examined 17 studies 

and reported that recovery rates were faster in disturbed and 

channel mud habitat communities that originally comprised 

small opportunistic taxa. They noted that habitats that were 

originally dominated by larger, long-lived taxa had much 

slower recovery times (up to 12 years).

Structural metrics such as the density and taxonomic 

composition of benthic organisms at a site are often used 

to assess benthic recovery; however, they may not be very 

meaningful if they lack relationships to ecological functions 

of interest in the impacted habitat (Wilber and Clarke, 

2007), such as prey productivity for consumers. Measures 

of ecological function, such as macroinvertebrate biomass, 

secondary production (amount of energy generated by a 

species assemblage; Brey and others, 1988), and functional 

diversity (for example, presence of multiple foraging guilds) 

of the community, provide information on the role benthic 

macroinvertebrates play in the ecosystem and may recover 

independently from structural metrics (Bolam, 2012, 2014). 

Thus, there is a growing interest in applying structural and 

functional metrics to evaluate recovery of habitat quality 

after a disturbance event (Clarke and others, 1993; Rodil and 

others, 2013; Bolam, 2014).
6 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Measuring Structural and Functional Recovery

Assessments such as the U.S. Fish and Wildlife Service 

(USFWS) Habitat Evaluation Procedure (HEP; U.S. Fish 

and Wildlife Service, 1980), Estuarine Habitat Assessment 

Protocol (Simenstad and others, 1991), and the Benthic 

Resources Assessment Technique (BRAT; Lunz and Kendall, 

1982; LaSalle, 1990) have been developed and used to 

evaluate functional recovery of the benthos. The BRAT 

assessment was specifically developed by the USACE to 

be used as a quantitative tool for evaluating and comparing 

dredge impacted sites in terms of trophic support for bottom 

feeding fishes (Lunz and Kendall, 1982; LaSalle, 1990). The 

BRAT approach has traditionally been used to determine the 

most suitable location to dispose of dredge material (Lunz 

and Kendall, 1982; Clarke, 1986), and it has also been applied 

to assessments of benthic prey availability for fish (Rhoads 

and Germano, 1986). Because BRAT integrates information 

on fish foraging ecology, prey biomass and energy content to 

estimate trophic (nutritional) support available for fishes in 

benthic habitats, we applied this framework with modifications 

to evaluate the impacts of periodic dredging on benthic 

communities compared to undredged reference areas. Our 

study considered the foraging needs of target fish species that 

were identified under the 2011 Programmatic EFH Agreement. 

In addition, we evaluated benthic macroinvertebrate density 

and community taxonomic composition between dredged 

and undredged reference areas as structural measures of 

habitat. Here we present synthesized results from the full 

study evaluating habitat quality for SFB benthic foraging fish 

in relationship to (1) dredged versus undredged locations, 

(2) distance to dredged site, and (3) years since dredging.

Methods

Study Design

Modified Benthic Resources Assessment 

Technique (MBRAT) Framework

The BRAT framework (fig. 1) integrates information 

on fish foraging ecology and prey profitability to estimate 

the energy that is available to specific fish feeding guilds. 

Prey profitability is a measurement that has been used to 

evaluate habitat quality for many benthic foraging predators 

(Richman and Lovvorn, 2004; Goss-Custard and others, 

2006; Lovvorn and others, 2013), including fish (Crowder 

and Cooper, 1982; Godin and Keenleyside, 1984). Energy 

content, size, and accessibility (visibility, vertical distribution 

in the sediment, predator defense, and escape capabilities) 

of macroinvertebrates are integral to determining their 

profitability to benthic foraging fish (Lunz and Kendall, 1982; 

Piet and others, 1998; van Denderen and others, 2013).

We modified the BRAT framework to address our study 

objectives, budget, and scope. This modified BRAT (hereafter, 

MBRAT) approach used benthic fish foraging ecology and 

diet information identified in our literature review and by 

local expert opinion (table 1; De La Cruz and others, 2017), 

in lieu of conducting a fish diet study. For each focal fish 

species, we considered the following factors for juveniles 

and adults: common prey taxa, foraging mode, foraging 

depth in the benthic subsurface, and maximum prey size 

(tables 1–2). Many benthic-foraging fishes are generalists, 

and consumption of macroinvertebrate prey items is related 

to local macroinvertebrate prey density, biomass, and 

vertical distribution. Therefore, we adjusted the MBRAT 

to include sorting and identifying macroinvertebrates into 

broad taxonomic categories instead of identifying to lowest 

taxonomic unit possible. Clarke (1986) found that similar 

modifications to broad levels of taxonomic identification 

were sufficient for BRAT in previous studies. However, we 

identified macroinvertebrates to species or lowest taxonomic 

unit in a random subset of core samples from each study site 

to enable comparison of structural metrics across sites.

Another modification to the traditional BRAT approach 

was dividing benthic core samples into two depths: shallow 

(0–4 centimeters [cm]) and deep (4–10 cm), rather than 

partitioning in 2-cm increments. This modification was 

based on our pilot study where we found that the majority of 

macroinvertebrates in cores from two pilot sites were located 

in the upper 4 cm of the core (fig. 2; De La Cruz and others, 

2017). Furthermore, other studies of fish prey have identified 

the best sample depth as that which approximately matches the 

predator's foraging depth (Ferraro and Cole, 2004). Although 

skates, sturgeon, leopard sharks, and crabs can forage 

relatively deep within the sediment (here represented as the 

entire core 0–10 cm depth), other target fish in our study (such 

as, sardine, anchovy, brown rockfish, and others) are primarily 

epi-benthic and near-surface feeders, which corresponds to 

the shallow portion of our cores (0–4 cm depth; Gotshall, 

1977; Holland and others, 1980; Bottom and Jones, 1990; 

tables 1–2). Thus, in our simplified scheme for evaluating prey 

accessibility (table 2), the upper 0–4 cm of the core represents 

the foraging area of target species such as sardine, anchovy, 

and brown rockfish, whereas deeper (4–10 cm) portions of the 

core represent the additional area available to species such as 

skates, sturgeon, leopard sharks, and crabs (table 2).
Methods 7

Figure 1. The Benthic Resource Assessment Technique (BRAT) outlines the activities to relate 

the resource value of benthic macroinvertebrates to fish predators (modified from Rhoads and 

Germano, 1986).
8 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 2. Simplified foraging table for focal fish species showing the depth increments and prey class sizes used in 

the MBRAT assessment.

[Depth and size class categories were derived based on information discussed in the Phase I Literature Review and summarized in table 3. 

Estimated available mean biomass (gram per square meter; g/m2) in dry weight (dw) and energy (kilojoule per square meter; kJ/m2) for 

each fish species and age class were calculated across all study sites and sampling dates for the appropriate depth and prey size class. *The 

50–100 millimeter (mm) size class can be consumed by some fish species; however, this study did not detect any macroinvertebrates in the 

50–100 mm size class. Abbreviations: %, percent; cm, centimeter]

Fish species Life 

stage

Prey size 

class 

(mm)*

Available prey 

biomass (g/m2 dw)

% biomass 

reduction from 

undredged to 

dredged

Available prey 

energy (kJ/m2)

% energy 

reduction from 

undredged to 

dredged Dredged Undredged Dredged Undredged

Foraging depth in sediment: Shallow (0–4 cm)

Pacific sardine Juvenile 0–4 3.04 5.40 44 50.23 89.22 44

Adult 0–24 26.62 41.02 35 126.96 212.43 40

Longfin smelt Juvenile 0–4 3.04 5.40 44 50.23 89.22 44

Adult 0–24 26.62 41.02 35 126.96 212.43 40

Northern anchovy Juvenile 0–4 3.04 5.40 44 50.23 89.22 44

Adult 0–100 30.04 48.86 39 137.99 237.46 42

English sole Juvenile 0–12 5.95 12.05 51 60.02 112.94 47

Adult 0–50 30.04 48.86 39 126.96 212.43 40

Starry flounder Juvenile 0–12 5.95 12.05 51 60.02 112.94 47

Adult 0–100 30.04 48.86 39 137.99 237.46 42

Brown rockfish Juvenile 0–4 3.04 5.40 44 50.23 89.22 44

Adult 0–100 30.04 48.86 39 137.99 237.46 42

California halibut Juvenile 0–50 30.04 48.86 39 126.96 212.43 40

Adult 0–100 30.04 48.86 39 137.99 237.46 42

Foraging depth in sediment: Deep (0–10 cm)

Dungeness crab Juvenile 0–100 33.44 56.97 41 154.66 310.11 50

Adult 0–100 33.44 56.97 41 154.66 310.11 50

Big skate Juvenile 0–100 33.44 56.97 41 154.66 310.11 50

Adult 0–100 33.44 56.97 41 154.66 310.11 50

Green sturgeon Juvenile 0–100 33.44 56.97 41 154.66 310.11 50

Adult 0–100 33.44 56.97 41 154.66 310.11 50

White sturgeon Juvenile 0–100 33.44 56.97 41 154.66 310.11 50

Adult 0–100 33.44 56.97 41 154.66 310.11 50

Leopard shark Juvenile 0–100 33.44 56.97 41 154.66 310.11 50

Adult 0–100 33.44 56.97 41 154.66 310.11 50
Methods 9

Figure 2. Mean density of benthic macroinvertebrates by 2-centimeter depth increments at dredged and undredged reference areas 

sampled at Mooring Road and Pier 32 sites during the pilot study.

Maximum macroinvertebrate prey sizes are largely 

unknown for the focal fish species in this study, especially for 

certain life stages (juveniles versus adults). For instance, most 

fish will consume different prey in juvenile compared to adult 

stages (such as, green and white sturgeon, California halibut; 

Haaker, 1975; Plummer and others, 1983; Muir and others, 

1988), and spatiotemporal patterns in prey availability can 

induce prey switching in certain fishes (Toole, 1980; Blaxter 

and Hunter, 1982). While some fish are expected to be able 

to consume prey as large as 100 millimeters (mm), such prey 

are likely to be small fishes or other highly mobile taxa, the 

sampling of which was outside the scope of our study. We did 

not encounter macroinvertebrates >50 mm in our samples, 

even though individuals of this size can be detected with 

our sampling gear. Thus, after extensive literature review 

(De La Cruz and others, 2016) and expert consultation with 

Dr. James Hobbs (University of California Davis, oral and 

written commun., 2014, 2017), Dr. Scott Hamilton (Moss 

Landing Marine Laboratory, oral and written commun., 

2017), and Dr. Fred Feyrer (USGS California Water Science 

Center, written commun., 2017), we established four unique 

macroinvertebrate size classes that encompassed the prey 

sizes that could be consumed by target fish species in our 

study: 0 to 4 mm, greater than 4 mm to 12 mm, greater 

than 12 mm to 24 mm, and greater than 24 mm to 50 mm 

(table 2). Macroinvertebrates were sorted into size classes 

based on overall body length for most taxa and head width for 

polychaetes and oligochaetes. Diet and foraging information 

(prey taxa, foraging depth in sediment, and maximum prey 

size) for adult and juvenile focal fish species gathered during 

the literature review were used to evaluate macroinvertebrate 

prey availability for each species and life stage at each 

study site.
10 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Taken together, the components of the MBRAT method 

create a framework to assess density, biomass, energy content, 

and vertical distribution for each broad macroinvertebrate 

taxa group and size class and we used this information to 

determine prey availability for each focal fish species (fig. 3, 

table 2). Implicit to this framework is the idea that an increase 

in biomass and (or) energy content of prey (as in, trophic 

support) that is the right size and depth to be available for 

a particular target species means that there is an increase in 

habitat function for that species.

Study Area and Site Selection

San Francisco Bay is a shallow estuary (median depth 

1.83 m below MLLW; Conomos and others, 1985) with four 

major sub-bays: Suisun Bay, North Bay (San Pablo Bay), 

Central Bay, and South Bay (fig. 4). We collected data for the 

initial power analyses conducted in this study from a 1.25 

square kilometer (km2) intertidal mudflat located in the South 

Bay (Dumbarton mudflat, 37°50’ N., 122°12’ W.; fig. 5). The 

South Bay is mesohaline (Thompson and others, 2013) with 

mixed semidiurnal tides ranging up to 3 m (Shellenbarger and 

others, 2013) such that the mudflat is inundated and exposed 

twice daily. The width of the Dumbarton mudflat increases 

from 200 to 900 m from north to south, and mudflat width is 

correlated with net deposition and erosion patterns throughout 

South Bay (van der Wegen and others, 2017). The Dumbarton 

mudflat extends about 1 km from shore to the channel and 

ranges in elevation from about –1.21 m to 1.11 m North 

American Vertical Datum 1988 (NAVD 88). Water column 

salinity during flood tides at the site ranged from 18 parts per 

thousand (ppt) in March and April to 32 ppt in late August 

and September.

Sampling sites for the pilot and full studies were 

located within and adjacent to marinas in the Central Bay, a 

predominantly polyhaline zone (1–30 ppt; fig. 6; Thompson 

and others, 2007, 2013; Gillet and others, 2014), which is 

generally characterized by fine-grained (silt and clay) to 

coarser sediments (sand and shell fragments; Goals Project, 

1999; Subtidal Goals Project, 2010; Barnard and others, 2013; 

Greene and others, 2013). Selected study site marinas were all 

less than 4 m deep, and the substrate consisted mostly of silt 

and clay (table 3). Sites were also most recently dredged in 

2013, 2014, or 2015 with a dredging frequency of 2–4 years, 

though some sites had a longer span of time between dredging 

such as Strawberry Channel (7 years), Loch Lomond Marina 

(12 years), and Mooring Road (infrequent).

Figure 3. Conceptual diagram illustrating differences in prey consumption for focal foraging fish species and between juvenile 

and adult fish (for example, English sole versus a leopard shark). Expected prey accessibility is based on depth within the 

sediment and macroinvertebrate size. A 10-cm sediment core is partitioned into two depth strata (0–4 cm and 4–10 cm), and 

different size classes of macroinvertebrates are represented by colored circles of variable dimensions.
Methods 11

Figure 4. Study sites in central San Francisco Bay. Red sites were dredged in 2015, orange sites were 

dredged in 2014, and green sites were dredged in 2013.
12 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Figure 5. Sampling locations in the Dumbarton Shoals mudflat adjacent to pond RSF2 in the Ravenswood complex of 

the South Bay Salt Pond Restoration Project.
Methods 13

Table 3. Central Bay site selection table indicating all sites considered for the pilot and full study.

[MLLW, mean lower low water; ft/m, foot per meter; SFB, San Franciso Bay; HOA, Homeowners Association]

Study area Location Embayment Salinity regime1 Habitat type Sediment 

texture

Dredge 

depth 

MLLW 

(ft/m)

Last 

dredged

Estimated 

dredging 

frequency 

(years)

Selected sites

2Pier 32 San Francisco Central SFB Polyhaline Shallow subtidal Sand/silt/clay 12.0/3.7 2013 2–3

Mooring Road3 San Rafael San Rafael Bay Poly/mesohaline Marina Silt/clay 6.0/1.8 2013 Infrequent

Richardson Bay 

Marina3

Sausalito Richardson Bay Polyhaline Marina Silt/clay 10.5/3.2 2013 3

Paradise Cay 

HOA3

Paradise Cay Corte Madera Bay Polyhaline Channel Silt 8.0/2.4 2014 4

Strawberry 

Channel3

Strawberry Richardson Bay Polyhaline Channel Silt/clay 7.0/2.1 2014 7

Loch Lomond 

Marina4

San Rafael San Rafael Bay Poly/mesohaline Marina Silt/clay 9.0/2.7 2015 12

Paradise 

Cay Yacht 

Harbor4

Paradise Cay Corte Madera Bay Polyhaline Marina Silt 10.0/3.0 2015 4

Sites considered, but not selected

Aeolian Yacht 

Club

Alameda San Leandro Bay Polyhaline Marina Clay 10.0/3.0 2014 4

Larkspur 

Marina

Larkspur Corte Madera Bay Polyhaline Marina Silt/clay 6.0/1.8 2015 4–5

Marina Vista 

HOA

San Rafael San Rafael Bay Poly/mesohaline Channel Silt/clay 7.0/2.1 2015 4

Marin Yacht 

Club

San Rafael San Rafael Bay Poly/mesohaline Marina Silt/clay 9.0/2.7 2016 5

SF Marina West 

Basin

San Francisco Central SFB Polyhaline Shallow subtidal Sand/silt/clay 13.0/4.0 2014 2–3

Clipper Yacht 

Harbor

Sausalito Richardson Bay Polyhaline Marina Silt/clay 9.0/2.7 2015 3–4

Corinthian 

Yacht Harbor

Sausalito Belvedere Cove Polyhaline Marina Silt/clay 13.0/4.0 2015 4

Larkspur Ferry 

Terminal

Larkspur Corte Madera Bay Polyhaline Channel Silt/clay 17.0/5.2 2015 4

1Thompson and others, 2013.

2Sites sampled for pilot study only.

3Sites sampled for pilot study and full study.

4Sites sampled for full study only.

We selected recently dredged marinas that had adjacent 

corresponding undredged reference areas. Here we used the 

term “reference” to refer to an area that was undredged, rather 

than a pristine site. It is important to note that the reference 

areas we selected are not “undisturbed.” Rather, undredged 

reference areas included similar localized environmental 

characteristics (salinity, depth, sediment texture) to the 

associated dredged marina, as well as ambient levels of 

disturbance to the sediment, including those associated with 

boat traffic, that are expected to occur in undredged areas of an 

urbanized estuary.
14 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

We compiled site characterization information for each 

marina (Bay Conservation and Development Commission, 

unpub. data, 2015, 2016) to inform decisions about sampling 

design elements (table 3). The primary site selection criteria 

were based on identified project objectives and included 

(1) location within the polyhaline region of the Central Bay 

(fig. 6); (2) post-dredging depth of <13 feet (4 m) MLLW; 

(3) predominantly soft-bottom sediments; (4) a dredging 

date falling within one of three time periods: 1 year before 

present, 2 years before present, and 3 years before present; 

and (5) presence of an adjacent undredged reference site. 

Undredged reference sites were considered areas near the 

study marina with no record of dredging that had similar 

environmental conditions to their corresponding dredged area. 

Time since dredging categories were chosen to meet the study 

objective of evaluating differences in areas “that are dredged 

at a frequency of annually to every three years compared to 

those that are undredged,” which was established by LTMS 

agencies during the study planning period.

Figure 6. San Francisco Bay benthic assemblages (Thompson and others, 2013). We 

focused on the polyhaline benthic assemblage in Central Bay. The average salinity in this 

assemblage is 30.4 parts per thousand. Sub-clusters eight and nine are dominated by the 

amphipods, Ampelisca abdita and Monocorophium acheruscium, and sub-cluster eight has 

high densities of polychaetes, Mediomastus spp. and Dorvillea (Schistomeringos) annulata.
Methods 15

For our pilot study, we selected sites Pier 32, Mooring 

Road, Richardson Bay Marina, Paradise Cay HOA, and 

Strawberry Channel (table 3, figs. 7–11). Pilot study samples 

from both the undredged and dredged areas at Pier 32 

indicated the site was dominated by polychaetes, which 

differed from the overall community composition at the 

other sampling sites (De La Cruz and others, 2017). This 

site was also the farthest south of the five pilot sites, and 

although still in the polyhaline region of San Francisco Bay, 

may have environmental conditions that differ from sites to 

the north. To reduce the variability that could be related to 

a non-representative study site, we removed Pier 32 from 

our site list, retained the other pilot study sites, and added 

two additional sites, Loch Lomond Marina and Paradise Cay 

Yacht Harbor (hereafter Yacht Harbor; both dredged in 2015; 

figs. 12–13), for a total of six study sites for the full study. 

Among the six marinas chosen for the full study, there were 

two marinas in each of three dredging time periods: 2013, 

2014, and 2015. These sites were evenly divided among three 

embayments within the Central Bay polyhaline region (fig. 6).

Power Analyses

After an extensive search during our Phase I literature 

review, we were unable to locate an appropriate existing 

Central Bay macroinvertebrate dataset to use in a power 

analysis to inform the study design. Therefore, we used a 

comprehensive USGS macroinvertebrate dataset collected 

monthly from October 2008 to April 2010 on mudflat and 

subtidal shoals southwest of the Dumbarton Bridge (fig. 5) as 

a proxy for the expected variability in the Central Bay.

We used a data-derived, simulation-based power analysis 

that was designed to consider variation within replicates 

and transects to inform the total number of transects and 

cores in our sampling design. In the initial step of our power 

analysis, we used an information-theoretic model selection 

framework (Akaike’s information criterion [AIC]; Burnham 

and Anderson, 2002) to identify the most parsimonious model 

for each taxon. We separately modeled densities of each broad 

taxa group using linear mixed models (PROC Mixed, SAS 9.3, 

SAS Institute Inc., Cary, North Carolina, U.S.A.). We used 

normal approximation models where the dependent variable 

was the log-transformed count (x + 0.5) for each taxon. 

We built the same candidate set of models for each taxon 

that included all possible combinations of month and year, 

elevation, and the interaction of these terms as fixed effects 

and included site, the number of transects, and the number of 

cores as random effects.

For each taxon, we identified the top model with 

the lowest AIC score and used the parameter estimates 

for the fixed and random effects from that model as input 

parameters for simulation models. Datasets were simulated for 

10 different sample sizes representing different combinations 

of sites, transects, core locations, and core replicates (table 4). 

Because the Dumbarton dataset represents an undredged site 

with no equivalent paired dredged site, we used scenarios to 

simulate hypothesized macroinvertebrate reductions of 0, 25, 

50, and 75 percent owing to dredging. For each taxonomic 

group, we ran 1,000 simulations per sample size and reduction 

scenario and calculated power as the proportion of simulations 

in which a significant effect (α=0.05) was detected.

Using the data collected in our pilot study, we conducted 

a second power analysis to determine if the number of 

samples originally identified based on South Bay Dumbarton 

site macroinvertebrate data were appropriate for a Central 

Bay study given the potential differences in taxa between 

the two areas. We used the methods described above for the 

initial power analysis prior to the pilot study and updated 

the taxonomic groups detected in the pilot study to include 

Amphipoda, Bivalvia, Cumacea, Isopoda, Nematoda, 

Oligochaeta, and Polychaeta. We simulated datasets based 

on 0, 25, 50, and 75 percent reduction in macroinvertebrate 

counts between undredged reference and dredged areas using 

levels of sampling variation in the pilot study.

For both power analyses, we used 80 percent power 

(Steidl and others, 1997; Quinn and Keough, 2002; 

Di Stefano, 2003) as the minimum acceptable value for 

identifying a difference in macroinvertebrate density between 

dredged and undredged areas. In both analyses, we found 

that power generally increased for all taxa as the number of 

samples increased (figs. 14–15). In the initial analysis using 

the Dumbarton dataset, power to determine a 50 percent 

reduction in density reached >80 percent under the scenario 

containing 200 cores for all taxa except errant polychaetes, 

which did not reach 80 percent power until the sample size 

was 320 cores (fig. 14). Power to determine a 25 percent or 

less difference between dredged and undredged sites was low 

for several taxa and did not reach 80 percent power for most 

taxa even at a sample size of 400 cores (fig. 14).

In the second power analysis using the pilot study 

dataset, power to determine a 50 percent reduction in density 

reached >80 percent under the scenario containing 100 cores 

for all taxa except for amphipods and polychaetes, which both 

reached 80 percent power with a sample size of 200 cores 

(fig. 15). For bivalves, cumaceans, isopods, and nematodes, 

the power to determine a 25 percent or less difference between 

dredged and undredged sites reached 80 percent power with 

a sample size of 200 cores; however, oligochaetes only 

reached 80 percent under 400-core scenarios, and amphipods 

and polychaetes did not reach 80 percent at any sample 

size (fig. 15).
Figure 7. Paradise Cay Homeowners Association (HOA) study site composed of residential docks and berths in western San Francisco Bay. Samplepart of the pilot and full study. The white outlined area was dredged to 8 feet mean lower low water (MLLW) in 2014. The site contains 24 core locationdredged area and 21 undredged reference core locations collected along 3 transects of 6 core locations in dredged marina, 1 transect of 6 core locatdredged entrance channel, 1 reference transect of 6 core locations with 3 transects of 5 core locations extending from reference transect to dredged channel transect.
Methods 17

Figure 8. Strawberry Channel study site composed of residential docks and berths in dredged channel 

through residential area and Aramburu Island in Richardson Bay. Sampled as part of the pilot and full 

study. The white outlined area was dredged to 7 feet mean lower low water (MLLW) in 2014. The site 

contains 10 core locations in the dredged area and 12 undredged reference core locations collected 

along 1 transect of 10 core locations and 1 transect of 7 core locations in the dredged marina/channel, 

1 reference transect of 7 core locations with 3 transects of 5 core locations extending from reference 

transect to dredged entrance channel transect.

Sampling Design

Given the scope and budget of the study, we determined 

that a design to detect a 50 percent reduction in individuals 

between dredged and undredged areas was most feasible. 

Thus, we designed the sampling effort to meet or exceed 

the 200-core sample size identified by the pilot data power 

analysis as robust for all taxonomic groups. Within each 

marina, we placed two to six transects in each dredged 

and undredged location. From each transect, we sampled a 

minimum of six core locations with two replicate samples 

taken at each core location (figs. 7–13).

Sampling was conducted seasonally in winter and 

summer to assess the greatest differences in seasonal variation 

in macroinvertebrate density and biomass. The inclusion 

of multiple collection periods enabled us to compare 

macroinvertebrate density and community composition during 

wet and dry seasons and across a range of seasonal salinities—

one of the major drivers of macroinvertebrate community 

composition (Nichols and Pamatmat, 1988; Thompson and 

others, 2013; De La Cruz and others, 2016). The summer 

sampling periods overlapped with the period of peak fish 

densities in the Central Bay and provided information on 

macroinvertebrate densities when most focal fish species 

were present (De La Cruz and others, 2016). To evaluate the 

effect of time-since-dredging on trophic support for fishes, we 

measured macroinvertebrate density and biomass at marinas 

that had been dredged 1, 2, and 3 years prior to sampling. 

To assess the effect of distance to nearest dredge site on 

macroinvertebrate density and biomass, we evenly spaced 

sampling locations within each transect 20 m apart from each 

other and ran transects perpendicular to dredged areas so 

that distances up to 120 m away from dredged areas could 

be evaluated.
18 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Figure 9. Richardson Bay Marina study site composed of marina docks and an undredged reference 

area northeast of the marina. Sampled as part of the pilot and full study. The white outlined area was 

dredged to 10.5 feet MLLW (mean lower low water) in 2013. The site contains one transect of 10 core 

locations taken in the dredged area between docks and another transect of 10 core locations in the area 

between docks that was dredged in 1994. Two reference transects of six core locations each extend from 

the marina.

Sample Processing

Sample Collection

We conducted sampling during two wet (as in, winter) 

and two dry (as in, summer) time periods throughout the 

course of the study: November 2015–December 2015 (pilot 

sampling), August 2016, January 2017, and August 2017. 

Based on our sampling design, each site had two to six 

transects per dredged and undredged site in a marina and a 

minimum of six core locations per transect. Two replicate 

core samples were collected at core locations set 20 m apart 

along each transect. Each core was 10 cm in diameter and 

10 cm deep. Cores were systematically separated into shallow 

(0–4 cm) and deep (4–10 cm) increments to measure prey 

distribution at different depths in the sediment according to 

MBRAT methodology (figs. 1, 3).

Upon arrival to and departure from sampling sites, water 

quality (temperature, salinity, dissolved oxygen, and pH) 

was recorded within dredged and undredged areas of each 

marina using a multi-parameter sonde (YSI Professional 

Plus, YSI, Inc., Yellow Springs, Ohio) just above the benthic 

surface in the demersal zone. The water depth at individual 

core locations along each transect was recorded using a 

ReefNet© Sensus Ultra Depth Recorder (ReefNet, Inc., Niagra 

Falls, New York) attached to the coring device and corrected 

for MLLW tide height at the time of recording. Sediment cores 

were collected at the mid-point of each transect and sent to an 

external laboratory (AandL Western Laboratories, Modesto, 

California) to determine sediment grain size and chemical 

composition (organic matter, sediment texture, sediment pH).
Methods 19

Figure 10. Port of San Francisco Pier 32 study site composed of an area between piers 32 and 36 in San Francisco. This site was 

only sampled as part of the pilot study. The white outlined area was dredged to 12 feet MLLW (mean lower low water) in 2013. The 

site contains 12 core locations in the dredged area and 18 undredged reference core locations collected along 2 transects of 6 core 

locations in the dredged marina/channel and 3 parallel transects of 6 core locations in the reference area between the dredged area 

and the shore.

Cores were immediately transported to the USGS 

Invertebrate Ecology Laboratory on ice and refrigerated until 

processed. Within 1–2 days, cores were rinsed through a 

500-micrometer (μm) mesh sieve, and fauna were retained 

by the sieve were preserved in a 70 percent ethanol with 

1 percent rose bengal dye. All taxa within cores were sorted, 

identified, and enumerated. During all sampling periods except 

the pilot (November–December 2015), macroinvertebrates 

were sorted into four size-classes based on target fish foraging 

ecology: 0–4 mm, 4–12 mm, 12–24 mm, and 24–50 mm. 

Taxa from all samples were identified to a broad taxonomic 

level (class, order); however, macroinvertebrates in six 

cores that were randomly selected from each site (three from 

dredged locations and three from undredged locations) during 

each sampling period were identified to the lowest possible 

taxonomic level (family, genus, species). We determined the 

number of cores in which macroinvertebrates were identified 

to the lowest possible taxonomic level by processing multiple 

cores from each pilot sampling site until the number of new 

species found reached an asymptote.

Internal laboratory quality control measures included 

resorting and identifying a minimum of 10 percent of 

samples by a technician with equivalent or greater experience 

compared to the original sorter. This process was repeated 

until maximum error percentages were less than 10 percent 

for each sorter. We also sent sorted taxa from two randomly 

selected cores from each marina and time period to an 

external laboratory (EcoAnalysts, Inc., Moscow, Idaho) 

for identification to lowest taxonomic level. This was done 

both as a quality assurance measure to verify our in-house 

identification and to build a reference collection for more rapid 

and precise identification of future samples.
20 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Figure 11. Mooring Road study site composed of dredged areas around residential docks in tidally 

influenced San Rafael Creek. Sampled as part of the pilot and full study. The white outlined area was 

dredged to 6 feet MLLW (mean lower low water) in 2013. The site contains 7 core locations in the dredged 

area and 12 undredged reference core locations collected along 1 transect of 7 core locations in dredged 

areas and 1 transect of 12 reference core locations that runs parallel to the dredged transect for 7 core 

locations and continues downstream from dredging for 5 core locations.

Macroinvertebrate Density, Biomass, and 

Energy Estimations

The density of macroinvertebrates at each core depth 

from each taxon and size class was calculated by averaging 

the densities from two replicate cores. Using the six cores 

from each site and season in which macroinvertebrates 

were identified to the lowest possible taxonomic level, we 

calculated the proportion of each lower taxonomic group 

within each broad taxonomic group for each size class, 

treatment (dredged or undredged), and site. We multiplied 

these proportions by the densities of each broad taxonomic 

group in each size class and treatment observed in the 

remaining cores at each site to obtain an estimated density for 

each lower-taxonomic group in each size class and treatment. 

Next, we multiplied the observed (from the six cores identified 

to lowest taxonomic level) and estimated (from the remaining 

cores identified to broad taxonomic level) densities of 

macroinvertebrates in each taxonomic group and size class by 

the mean biomass per individual of that taxon and size class.

To determine mean biomass per individual for a given 

taxon and size class, macroinvertebrates were dried in a 

precision convection oven at 80 degrees Celsius (°C) for 

24 hours and weighed with an A and D Weighing HR-202i 

semi microbalance (0.1 mg; Abington, Oxfordshire, United 

Kingdom). Biomass was estimated for the most abundant 

taxa (Actiniaria, Amphipoda, Bivalvia, Copepoda, Corixidae, 

Cumacea, Decapoda, Errantia polychaeta, Gastropoda, 

Isopoda, Leptostraca, Nemertea, Oligochaeta, Ostracoda, 

Sedentaria Polychaeta, Tanaidacea, Sipuncula, Tunicata). 

Because of their limited densities, it was not possible to 

measure biomass for rare taxa, but the biomass of these taxa 

was considered negligible. When a broad taxonomic group 

was not present in any of the cores identified to the lowest 

possible taxonomic level, we used the average biomass of all 

possible lower taxonomic groups within that broad taxonomic 

group. We determined secondary production of each site by 

calculating the energy available to benthic foraging fishes. We 

calculated macroinvertebrate energy content (in kilojoules, 

kJ) using published conversion factors (Cumminns and 

Wuycheck, 1971; Ricciardi and Bourget, 1998; Brey, 2001; 

Cauffope and Heymans, 2005) to convert dry biomass to 

ash-free dry biomass (AFDM) and AFDM to energy (kJ). 

Because biomass is size-dependent and macroinvertebrates 

were not separated into size classes during the pilot study, 

we did not calculate biomass or energy content for pilot 

study samples.
Methods 21

Figure 12. Loch Lomond Marina study site composed of a marina and entrance channel in San Rafael Bay sampled as part of the 

full study. The white outlined area was dredged to nine feet MLLW in 2015. The site contains 28 core locations in the dredged area 

and 20 undredged reference core locations collected along 4 transects of 4 to 7 core locations in the dredged marina, 1 transect 

of 6 core locations in the dredged entrance channel, 1 reference transect of 5 core locations, and 3 transects of 5 core locations 

extending from the reference transect to the dredged entrance channel transect.

Statistical Analyses

We evaluated differences in salinity, bathymetry, and 

sediment characteristics that could influence macroinvertebrate 

density and biomass among sites using general linear models 

(GLMs) and linear discriminant function (LDF) analysis. We 

tested differences in the elevations of core locations among 

sites and differences in average demersal zone salinity among 

sites and sampling periods using GLMs. Differences in 

sediment characteristics including pH, percent organic matter, 

percent sand, and percent silt were tested among sites and 

between dredged and undredged areas using LDF analysis 

with the package klaR (Weihs and others, 2005) in R v.3.4.1 

(R Development Core Team, 2017). We included percent 

clay in figures, but not in statistical analyses because percent 

sand, percent silt, and percent clay for a single sample add up 

to 100 percent. Thus, they were perfectly correlated so only 

two of the three variables could be included in analyses. All 

variables were centered and scaled prior to LDF, and statistical 

significance of sediment characteristics was determined 

with forward, stepwise selection using the Wilks’ Lambda 

(λ) criterion.
22 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Figure 13. Paradise Cay Yacht Harbor study site composed of a marina and entrance channel in western San Francisco Bay. 

Sampled as part of the full study. The white outlined area was dredged to 10 feet MLLW (mean lower low water) in 2015. The site 

contains 22 core locations in the dredged area and 21 undredged reference core locations collected along 3 transects of 5 to 6 

core locations in the dredged marina, 1 transect of 6 core locations in the dredged entrance channel, 1 reference transect of 6 core 

locations, and 3 transects of 5 core locations extending from the reference transect to the dredged entrance channel transect.

We assessed the effects of treatment (dredged 

versus undredged), time-since-dredging, and distance 

to the nearest dredged area separately on three response 

variables: (1) density (individuals per square meter [m2]), 

(2) dry biomass (grams per square meter [g/m2]), and 

(3) energy content (kilojoules per square meter [kJ/m2]) of 

macroinvertebrates using generalized linear mixed models 

(GLMMs) with the gamlss package (Stasinopoulos and Rigby, 

2007) in R v.3.4.1 (R Development Core Team, 2017). For 

each response variable, we ran GLMMs for five different 

datasets that represented the spectrum of macroinvertebrate 

prey available to benthic foraging fishes: (1) 0–4 mm 

macroinvertebrates in surface cores (0–4 cm deep); (2) 4–12 

mm macroinvertebrates in surface cores; (3) 12–24 mm 

macroinvertebrates in surface cores; (4) 24–50 mm 

macroinvertebrates in surface cores; and (5) 0–50 mm 

macroinvertebrates in whole cores (0–10 cm deep). For whole 

cores, macroinvertebrate size classes were combined because 

fish that could exploit this depth could also consume all prey 

sizes considered.

The GLMMs that tested the effects of treatment 

and distance to the nearest dredged area included 

macroinvertebrate data from cores collected in dredged 

and undredged areas, but GLMMs that tested the effect of 

time-since-dredging included data from cores collected in 

dredged areas only. The effect of distance to the nearest 

dredged area was tested to evaluate both the effect size of a 

dredged area, as well as to provide insight on species-specific 

recolonization of dredged sites from adjacent undredged 

areas. All GLMMs were run using a zero-adjusted gamma 

distribution because our macroinvertebrate datasets were 

zero-inflated. We included season, salinity, and elevation of the 

core location in all models as fixed effects. We determined the 

best random effects structure for GLMMs by comparing AIC 

scores among models with and without each of the random 

effects. Site and transect were included as random effects in 

GLMMs that tested the effects of treatment and distance to the 

nearest dredged area, and site was included as a random effect 

in GLMMs that tested the effect of time-since-dredging.
Methods 23

Table 4. Sampling scenarios used in simulation power analyses to determine 

project sample size. Scenarios had a variable number of sites (marinas), and 

each marina had one dredged and one undredged area.

[Scenarios had a variable number of sites (marinas), and each marina had one dredged and 

one undredged area. Within each of these areas we varied the number of transects, cores, and 

core replicates.]

Site 

(marina)

Areas 

(dredged and 

undredged)

Transects

(per area)

Cores

(per transect)

Replicates 

(per core)

Total number 

of core 

samples

2 2 2 2 2 32

3 2 1 5 3 90

5 2 2 5 1 100

5 2 1 5 3 150

5 2 2 5 2 200

5 2 1 8 3 240

5 2 2 5 3 300

5 2 2 8 2 320

10 2 2 5 2 400

5 2 2 10 2 400
24 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay Power

Scenario

Figure 14. Power analysis curves for individual taxa groups based on the comprehensive 

U.S. Geological Survey Dumbarton macroinvertebrate dataset. Scenarios depicted on the x-axis are 

for 10 simulated datasets (listed in table 1) representing different combinations of sites, transects, 

and replicate cores. The y-axis indicates the percent power to determine the difference between 

dredged and undredged areas. Colored lines represent macroinvertebrate reductions of 0 percent (red), 

25 percent (green), 50 percent (blue), and 75 percent (purple) owing to dredging.
Methods 25

Power

Scenario

Figure 15. Power analysis curves for individual taxa groups based on 

the 2015 pilot study macroinvertebrate dataset. Scenarios depicted on the 

x-axis are for 10 simulated datasets (listed in table 4) representing different 

combinations of sites, transects, and replicate cores. The y-axis indicates the 

percent power to determine the difference between dredged and undredged 

areas. Colored lines represent macroinvertebrate reductions of 0 percent 

(red), 25 percent (green), 50 percent (blue), and 75 percent (purple) owing 

to dredging.
26 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Results

Salinity, Elevation, and Sediment 

Characteristics Among Sites

Overall, demersal zone salinities measured during the 

winter sampling period of January 2017 were significantly 

lower at all sites than salinities measured during the other 

sampling periods (table 5), reflecting the unusually heavy 

rainfall from a series of atmospheric rivers during this season. 

Despite some significant differences in demersal zone salinity 

among sites (fig. 16; table 5), we observed the same general 

pattern at each site; salinities were lowest during the unusually 

wet January 2017 sampling period and were similar among the 

pilot sampling period (November–December 2015) and the 

two summer sampling periods (August 2016 and August 2017; 

fig. 16). Practical Salinity Unit (psu) measurements ranged 

from 2.37 at Mooring Road in January 2017 to 32.66 psu at 

Strawberry Channel in August 2016 (fig. 16). Demersal zone 

salinities at Richardson Bay and Strawberry Channel had the 

least seasonal variability (fig. 16). In contrast, large differences 

between summer and winter demersal salinities were observed 

at Mooring Road and Yacht Harbor (fig. 16).

Among sites, elevation of core locations ranged from 

–2.2 m to 0.3 m, with both the highest and lowest points 

at Yacht Harbor. We observed notable differences in core 

elevations among sites (table 6), but generally, elevations at all 

sites fell within a relatively narrow range (fig. 17). In addition, 

core elevations at dredged and undredged areas were similar 

within sites (fig. 17).

Sediment characteristics including percent organic 

matter, pH, percent sand, percent silt, and percent clay were 

not different between shallow (0–4 cm) and deep (4–10 cm) 

core segments within each site (figs. 18–23). Three sediment 

characteristics, percent silt (λ = 0.77, p < 0.001), percent 

sand (λ = 0.59, p < 0.001), and pH (λ = 0.49, p < 0.001), 

contributed significantly to an LDF that explained differences 

in sediments among sites (figs. 18–23). Percent silt ranged 

from 36.82 ± 1.00 (mean ± standard error) at Mooring Road 

to 48.16 ± 1.16 at Yacht Harbor. Percent sand ranged from 

14.41 ± 0.92 at Loch Lomond to 24.80 ± 1.28 at Richardson 

Bay, and mean pH ranged from 6.92 ± 0.07 at Strawberry 

Channel to 7.27 ± 0.03 at Loch Lomond. In addition, percent 

organic matter (λ = 0.84, p < 0.001), percent silt (λ = 0.81, 

p = 0.01), and percent sand (λ = 0.79, p = 0.02), contributed 

significantly to an LDF that explained differences in sediment 

between dredged and undredged areas. Percent organic matter 

and percent sand (2.97 ± 0.57 and 18.63 ± 0.88, respectively) 

were greater in dredged areas than in undredged areas 

(2.48 ± 0.05 and 17.51 ± 0.80), whereas percent silt was 

greater in undredged areas (47.69 ± 0.75) compared to dredged 

areas (42.58 ± 0.56; figs. 18–20). Despite these significant 

differences, sediment texture based on percent sand, silt, 

and clay was similar among sites and between dredged and 

undredged areas, with most sediments classified as loams with 

high percentages of silt or clay (fig. 23).

Table 5. General Linear Model (GLM) results for demersal 

salinity as a function of site (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and Yacht 

Harbor) and sampling period (November 2015, August 2016, 

January 2017, and August 2017).

[Loch Lomond is the reference site, and November 2015 is the reference 

sampling period for the analysis. Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

Z-value p

Intercept 28.731 1.850 15.534 <0.001

Site: Mooring Road –4.205 1.632 –2.577 0.013

Site: Paradise Cay –0.177 1.600 –0.111 0.912

Site: Richardson Bay 4.669 1.620 2.882 0.006

Site: Strawberry Channel 5.179 1.653 3.132 0.003

Site: Yacht Harbor –1.408 1.690 –0.833 0.409

Sampling 2016-8 0.919 1.574 0.584 0.562

Sampling 2017-1 –14.736 1.559 –9.454 <0.001

Sampling 2017-8 –0.513 1.574 –0.326 0.746

Table 6. General Linear Model (GLM) results for core elevation 

as a function of site (Loch Lomond, Mooring Road, Paradise Cay, 

Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Loch Lomond is the reference site for the analysis. Abbreviation: <, less 

than]

Fixed effect Estimate Standard 

error

Z-value p

Intercept –0.412 0.065 –6.368 <0.001

Site: Mooring Road 0.278 0.121 2.290 0.023

Site: Paradise Cay –0.537 0.093 –5.778 <0.001

Site: Richardson Bay –0.506 0.102 –4.951 <0.001

Site: Strawberry Channel 0.111 0.097 1.148 0.252

Site: Yacht Harbor –0.759 0.094 –8.073 <0.001
Figure 16. Summer and winter demersal salinity (psu) at six coring sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Loduring four sampling periods (November 2015, August 2016, January 2017, and August 2017). Boxes show values of the first and third quartiles around extend to 1.5-times the interquartile range.
Figure 17. Elevation (meters) in dredged (blue) and undredged (yellow) areas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, StrawLomond, and Yacht Harbor). Boxes show values of the first and third quartiles around the median. Whiskers extend to 1.5-times the interquartile range
Figure 18. Sediment organic matter content measured as percent loss on ignition in shallow (0–4 centimeters [cm]; purple) and deep (4–10 cm; yelloundredged areas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Franc
Figure 19. Percent silt in sediments from shallow (0–4 centimeters [cm]; purple) and deep (4–10 cm; yellow) cores of dredged and undredged areas Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay.
Figure 20. Percent sand in sediments from shallow (0–4 centimeters [cm]; purple) and deep (4–10 cm; yellow) cores of dredged and undredged area(Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay.
Figure 21. Percent clay in sediments from shallow (0–4 centimeters [cm]; purple) and deep (4–10 cm; yellow) cores of dredged and undredged areas (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay.
Figure 22. Sediment pH measured in shallow (0–4 centimeters [cm]; purple) and deep (4–10 cm; yellow) cores of dredged and undredged areas at siRoad, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay.
Figure 23. Sediment triangles used to classify sediment texture with percent sand, percent silt, and percent clay from sediments collected in dredgeundredged (yellow) areas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in SaBay. Textures abbreviations: Sand (Sa), Silt (Si), Clay (Cl), Loam (Lo).
Results 35

Within-Site Macroinvertebrate Community 

Composition, Density, Biomass, and 

Energy Content

We collected a total of 1,644 whole benthic cores: 

288 during the pilot sampling effort and 1,356 during the 

full study. We identified 33 broad taxonomic groups of 

macroinvertebrates among the 6 sampling sites and 4 sampling 

dates. Although the focus of our study was on the foraging 

value of broad taxonomic macroinvertebrate groups, we 

identified organisms from a random subsample of cores from 

each site to lowest taxa as a measure of structural recovery. 

We detected 104 distinct taxa in the shallow (0–4 cm) depth 

(table 7) compared to 43 taxa in the deep (4–10 cm) depth 

range (table 8). Within the surface sediments (0–4 cm), we 

generally found a greater taxonomic richness in undredged 

areas compared to dredged areas (undredged:dredge 

taxonomic richness ratio; 1.3 Loch Lomond, 1.4 Mooring 

Road, 1.2 Paradise Cay, 0.9 Richardson Bay, 1.5 Strawberry 

Channel, and 1.9 Yacht Harbor). In the shallow sediments 

of Richardson Bay, we detected greater taxonomic richness 

within dredged areas compared to undredged (dredge area 

59 taxa, undredged area 52 taxa). A similar pattern was also 

observed within deeper sections (4–10 cm) of the sediment 

profile where most sites had greater taxa richness in undredged 

areas (undredged:dredge taxonomic richness ratio; 0.9 Loch 

Lomond, 1.3 Mooring Road, 1.5 Paradise Cay, 1.0 Richardson 

Bay, 1.3 Strawberry Channel, and 1.7 Yacht Harbor). In the 

deep cores, we detected greater taxonomic richness within 

dredged areas compared to undredged at Loch Lomond 

(dredged area 12 taxa, undredged area 11 taxa).

During our study, we identified 13 adult specimens of the 

horseshoe shrimp (Lightiella serendipita), nearly doubling the 

number of known samples for this rare endemic Cephalocarid 

species. Thought to be extinct, this species has not been 

observed in SFB since 1988 (Jones, 1961; Schemel and others, 

1988, 1990), despite previous attempts to locate it during 

1997–99 (C. Rogers, University of Kansas, written commun., 

2017, 2018) and in 2000 (R. Mooi, California Academy of 

Sciences, written commun., 2017, 2018. Based on the number 

of samples we collected, L. serendipita had a detection rate 

of 0.5 percent, making this finding a truly serendipitous 

rediscovery of the species.

To facilitate statistical analyses and interpretation 

of functional foraging habitat characteristics for fish, we 

consolidated macroinvertebrates into broad taxonomic groups 

(Amphipoda, Bivalvia, Cumacea, Nematoda, Oligochaeta, 

Polychaeta, and other taxa). Macroinvertebrate cumulative 

community composition, density, biomass, and energy content 

varied somewhat among study locations (figs. 24–26; table 9). 

Macroinvertebrate densities were generally dominated by 

Polychaeta and Amphipoda and to a lesser extent Oligochaeta, 

Bivalvia, and Nematoda across all sites (fig. 24). On the other 

hand, macroinvertebrate biomass was clearly dominated by 

Bivalvia (especially at Mooring Road) and Polychaeta, with 

negligible contributions from other taxonomic groups (fig. 25), 

while Polychaeta contributed more substantially to energy 

content at each site (fig. 26). Below we summarize cumulative 

(calculated across all available sampling periods) site-specific 

trends in macroinvertebrate density, biomass, and energy 

content between dredged areas and their paired undredged 

reference areas.

Dredged in 2013

Overall, at Mooring Road macroinvertebrate density 

was 39 percent greater in undredged areas than dredged 

areas. Dominant taxa in dredged areas included bivalves 

(34 percent of the total density), polychaetes (24 percent), and 

oligochaetes (11 percent). In undredged areas, the community 

was predominated by polychaetes (30 percent) and bivalves 

(23 percent) and contained more oligochaetes (16 percent) 

relative to dredged areas. Biomass and energy content at both 

dredged and undredged areas in Mooring Road were driven 

primarily by bivalves and were 6 and nearly 2.5 times greater, 

respectively than the site with the next greatest biomass, Loch 

Lomond undredged (table 9; figs. 24–26).

Dredged and reference areas at the Pier 32 site sampled 

only during the pilot study were numerically dominated by 

polychaetes and contained more polychaetes than most other 

sites, except for the Paradise Cay dredged area. Polychaetes 

comprised 94 percent of the community in dredged areas 

and 78 percent in undredged areas, which also contained 

16 percent bivalves (fig. 27). Biomass and energy content of 

macroinvertebrates were not measured during the pilot study.

At Richardson Bay, overall density was 29 percent 

greater in undredged areas than in dredged areas (table 9). 

Dredged areas were dominated by polychaetes (56 percent) 

followed by nematodes (20 percent) and oligochaetes 

(10 percent). Macroinvertebrate communities in undredged 

areas were dominated by nematodes (37 percent) and 

polychaetes (27 percent), but amphipods (16 percent) were 

more abundant than oligochaetes (11 percent). Biomass at 

Richardson Bay was 124 percent greater in the undredged area 

than the dredged area but biomass was dominated by bivalves 

and polychaetes in both areas. In the dredged area, bivalves 

accounted for 62 percent of the biomass, while polychaetes 

accounted for 36 percent; in the undredged area, bivalves 

and polychaetes accounted for almost equal percentages of 

the biomass (49 percent and 47 percent, respectively; table 9; 

fig. 25). Overall, the undredged area provided 166 percent 

more energy for demersal fish than the dredged area (table 9; 

fig. 26). In both dredged and undredged areas, polychaetes 

provided the greatest proportion of the energy content 

(75 percent and 83 percent respectively; fig. 26).
36 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 7. Macroinvertebrate taxa identified in shallow (0–4 centimeters [cm];) cores from dredged (D) and undredged (U) locations at 

six sites—Mooring Road (MR), Richardson Bay (RB), Paradise Cay (PC), Strawberry Channel (SC), Loch Lomond (LL), and Yacht Harbor 

(YH)—in San Francisco Bay, California.

[In some cases, we identified to broader taxa (such as family) when pieces of organisms were encountered or when organisms were too small for distinguishing 

identifying features. Broader taxonomic categories are not included in total taxa count if they were represented by lower taxonomic identification (ID)]

Broad taxonomic group Lowest taxonomic ID Taxonomic 

rank

MR RB PC SC LL YH

D U D U D U D U D U D U

Actiniaria Actiniaria Order X X X X X X X X X

Amphipoda Ampelisca abdita Species X X X X X X X

Ampithoe Genus X X

Caprella Genus X X X X X

Corophiidae Family X X X X X X X X X X

Grandidierella japonica Species X X X X X X X X X X X

Monocorophium Genus X X X X X X X X X X X X

Paradexamine Genus X X X

Sinocorophium Genus X X X X

Annelida Annelida Phylum X

Bacillariophyceae Bacillariophyceae Class X

Bivalvia Arcuatula senhousia Species X X X X X X X X X X

Gemma gemma Species X X X X X X

Kurtiella tumida Species X

Macoma petalum Species X X X X X X X

Mya arenaria Species X X

Potamocorbula amurensis Species X X X X X X X X X X

Bivalvia Ruditapes philippinarum Species X X

Theora lubrica Species X X X X X X X

Other Bivalvia Class X X X X X X X X X X X X

Bryozoa Bryozoa Phylum X X X X X X X X X X

Cirripidea Cirripidea Subphylum X

Copepoda Cyclopoida Order X

Harpacticoida Order X X X X

Crustacea Crustacea Subphylum X X X X X

Cumacea Nippoleucon hinumensis Species X X X X X X X X X X X X

Cumella vulgaris Species X

Decapoda Cancridae Family X

Carcinus maenas Species X X

Gastropoda Aplysiopsis enteromorphae Species X

Haminoeidae Family X

Heterobranchia Subclass X

Hydrobiidae Family X X

Odostomia Genus X

Philine Genus X X

Potamopyrgus antipodarum Species X X

Volvulella Genus X

Hutchinsoniellidae Lightiella serendipita Species X X

Insecta Corixidae Family X
Results 37

Table 7. Macroinvertebrate taxa identified in shallow (0–4 centimeters [cm];) cores from dredged (D) and undredged (U) locations at 

six sites—Mooring Road (MR), Richardson Bay (RB), Paradise Cay (PC), Strawberry Channel (SC), Loch Lomond (LL), and Yacht Harbor 

(YH)—in San Francisco Bay, California.—Continued

[In some cases, we identified to broader taxa (such as family) when pieces of organisms were encountered or when organisms were too small for distinguishing 

identifying features. Broader taxonomic categories are not included in total taxa count if they were represented by lower taxonomic identification (ID)]

Broad taxonomic group Lowest taxonomic ID Taxonomic 

rank

MR RB PC SC LL YH

D U D U D U D U D U D U

Isopoda Gnorimosphaeroma oregonense Species X

Idotea Genus X

Paranthura japonica Species X X X X X X

Synidotea Genus X

Leptostracata Nebalia Genus X X X X

Nematoda Nematoda Phylum X X X X X X X X X X X X

Nemertea Nemertea Phylum X X X X X X

Oligochaeta Oligochaeta Subclass X X X X X X X X X X X X

Ophiuroidea Ophiuroidea Class X

Osteichthyes Osteichthyes Superclass X X X

Ostracoda Myodocopida Order X X X X X X

Podocopida Order X X

Rutiderma Genus X X

Pantopoda Pantopoda Order X

Porifera Porifera Phylum X X

Polychaeta (Errantia) Alitta Genus X X X

Dorvillea Genus X X X X X

Eteone Genus X X X X X X X X X X

Exogone lourei Species X X X X X X X X X X X

Glycinde Genus X X X X X X X X X

Harmothoe imbricate Species X

Hypereteone lighti Species X X X X X X X X

Malmgreniella macgintiei Species X X X X X

Megasyllis nipponica Species X X X X

Neanthes acuminata Species X

Nephtys Genus X X

Playtnereis bicanaliculata Species X X

Pettiboneia pugettensis Species X

Schistomeringos annulata Species X X X X

Schistomeringos longicornis Species X

Sphaerosyllis californiensis Species X

Syllidae Family X X X X X X X

Syllis nipponica Species X X

Polychaeta (Sedentaria) Armandia brevis Species X X X X

Capitella capitata Species X X X X X X

Capitellidae Family X X X X X X X X X X X

Chaetozone Genus X

Chone gracilis Species X

Cirratulidae Family X X X X X X X X X

Cirratulus dillonensis Species X
38 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 7. Macroinvertebrate taxa identified in shallow (0–4 centimeters [cm];) cores from dredged (D) and undredged (U) locations at 

six sites—Mooring Road (MR), Richardson Bay (RB), Paradise Cay (PC), Strawberry Channel (SC), Loch Lomond (LL), and Yacht Harbor 

(YH)—in San Francisco Bay, California.—Continued

[In some cases, we identified to broader taxa (such as family) when pieces of organisms were encountered or when organisms were too small for distinguishing 

identifying features. Broader taxonomic categories are not included in total taxa count if they were represented by lower taxonomic identification (ID)]

Broad taxonomic group Lowest taxonomic ID Taxonomic 

rank

MR RB PC SC LL YH

D U D U D U D U D U D U

Cirratulis spectabilis Species X

Cirriformia Genus X

Cirriformia moorei Species X X X X X

Cossura pygodactylata Species X X X X X X X

Euchone limnicola Species X X X X X X X

Heteromastus Genus X X X X

Leitoscoloplos pugettensis Species X X

Lumbrineridae Family X

Mediomastus Genus X X X X

Ophellidae Family X

Orbiniidae Family X X

Owenia collaris Species X

Pseudopolydora Genus X X X X

Sabaco elongatus Species X X X X X X X X X

Sabellidae Family X X

Spionidae Family X X X X X X X X X X X

Streblospio benedicti Species X X X X X X X X X X

Terebellidae Family X X

Sipuncula Sipuncula Phylum X X X X X X

Tanaidacea Chondrochelia dubia Species X X

Leptochelia Genus X X

Tunicata Ascidiidae Family X X

Molgula manhattensis Species X

Molgulidae Family X X

Unknown Unknown X X X X X X X X X X X X

Total taxa observed 22 37 54 56 30 43 29 46 27 33 18 39
Results 39

Table 8. Macroinvertebrate taxa identified in deep (4–10 centimeters [cm]) cores from dredged (D) and undredged (U) locations at 

six sites—Mooring Road (MR), Richardson Bay (RB), Paradise Cay (PC), Strawberry Channel (SC), Loch Lomond (LL), and Yacht Harbor 

(YH)—in San Francisco Bay, California.

[In some cases, we identified to broader taxa (such as family) when pieces of organisms were encountered or when organisms were too small for distinguishing 

identifying features. Broader taxonomic categories are not included in total taxa count if they were represented by lower taxonomic identification (ID)]

Broad taxonomic group Lowest taxonomic ID Taxonomic 

rank

MR RB PC SC LL YH

D U D U D U D U D U D U

Actiniaria Actiniaria Order X

Amphipoda Ampelisca abdita Species X X X X X

Corophiidae Family X

Grandidierella japonica Species X X X

Monocorophium Genus X X X

Annelida Annelida Phylum X

Bacillariophyceae Bacillariophyceae Order X X

Coscinodiscales Order X

Bivalvia Arcuatula senhousia Species X X X

Gemma gemma Species X X

Macoma petalum Species X X X

Bryozoa Bryozoa Phylum X X X X X X X X

Copepoda Copepoda Subclass X X X

Crustacea Crustacea Subphylum X

Cumacea Nippoleucon hinumensis Species X X X X X X X X X X X X

Gastropoda Gastropoda Class X

Hirudinea Hirudinea Subclass X

Hutchinsoniellidae Lightiella serendipita Species X X X

Insecta Corixidae Family X

Isopoda Paranthura japonica Species X X X X X

Leptostraca Nebalia Genus X X X

Nematoda Nematoda Phylum X X X X X X X X X X X

Oligochaeta Oligochaeta Subclass X X X X X X X X X X X X

Osteichthyes Osteichthyes Superclass X X X

Ostracoda Myodocopida Order X X

Pantopoda Pantopoda Order x

Polychaeta (Errantia) Alitta Genus X

Exogone lourei Species X

Glycinde Genus X X

Megasyllis nipponica Species X

Schistomeringos longicornis Species X

Polychaeta (Sedentaria) Capitella capitata Species X X

Capitellidae Family X X X X X X

Cirratulidae Family X X

Cirratulus dillonensis Species X

Cirriformia Genus X

Cirriformia moorei Species X X X

Cossura pygodactylata Species X X X X X X X

Leitoscoloplos pugettensis Species X
40 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Dredged in 2014

Macroinvertebrate density was 53 percent less in 

undredged areas than in dredged areas (table 9) at Paradise 

Cay. Polychaetes were dominant in dredged areas (72 percent), 

which also contained amphipods (17 percent). This differed 

from the undredged area at this site, which was dominated by 

amphipods (60 percent) and had notably fewer polychaetes 

(18 percent; fig. 24). Macroinvertebrate communities in the 

undredged area at Paradise Cay had the greatest density and 

percentage of amphipods relative to other sites. Biomass 

values in the dredged and undredged areas at Paradise Cay 

were similar (13.3 g/m2 dry weight [dw] in dredged area 

versus 13.8 g/m2 dw in undredged area; table 9). In the 

dredged area, polychaetes accounted for 72 percent of the 

biomass, while bivalves accounted for 24 percent; in the 

undredged area, polychaetes accounted for 28 percent of the 

biomass, while bivalves accounted for 59 percent (fig. 25). 

Overall, the dredged area provided 49 percent more energy 

than the undredged area (table 9), with polychaetes providing 

98 percent of the energy in the dredged area versus 58 percent 

in the undredged area (fig. 26).

Strawberry Channel macroinvertebrate densities in 

undredged areas were 136 percent greater than in dredged 

areas (table 9). Communities within the dredged areas at 

this site primarily consisted of polychaetes (38 percent), 

oligochaetes (23 percent dredged), and nematodes 

(13 percent). In the undredged areas, polychaetes (38 percent), 

oligochaetes (22 percent), and amphipods (20 percent) 

were the most abundant taxa (fig. 24). Strawberry Channel 

macroinvertebrate communities had the greatest percentage 

of oligochaetes at dredged and undredged areas relative to 

other sites. Biomass in the dredged and undredged areas at 

Strawberry Channel were similar (28.8 g/m2 dw in dredged 

area versus 31.1 g/m2 dw in undredged area; table 9). In 

the dredged area, bivalves accounted for 96 percent of 

the biomass; in the undredged area, however, polychaetes 

accounted for 19 percent of the biomass, while bivalves 

accounted for 79 percent (fig. 25). The undredged area 

provided 77 percent more energy than the dredged area 

(table 9). Polychaetes provided 54 percent of available energy 

in the undredged area, while bivalves supplied 41 percent 

and other taxa comprised the additional 5 percent. Bivalves 

provided 82 percent of available energy at the dredged area 

and polychaetes the remaining 18 percent (fig. 26).

Dredged in 2015

At Loch Lomond, macroinvertebrate densities in 

the undredged area were 219 percent greater than in the 

dredged area; the average density in the dredged area was 

the lowest among all the sites (table 9). Dominant taxa in the 

dredged area included polychaetes (24 percent), oligochaetes 

(18 percent), and nematodes (18 percent); the undredged area 

consisted mainly of polychaetes (32 percent), nematodes 

(22 percent), and amphipods (20 percent). Biomass at Loch 

Lomond was 171 percent greater in the undredged areas than 

in the dredged areas (table 9). In the dredged area, bivalves 

accounted for 90 percent of the biomass; in the undredged 

area, however, polychaetes accounted for 41 percent of the 

biomass, while bivalves accounted for 58 percent. Likewise, 

macroinvertebrate energy content in the undredged area was 

475 percent greater than in the dredged area, with polychaetes 

contributing 79 percent and bivalves 21 percent of the energy 

in the undredged area (fig. 26).

Table 8. Macroinvertebrate taxa identified in deep (4–10 centimeters [cm]) cores from dredged (D) and undredged (U) locations at 

six sites—Mooring Road (MR), Richardson Bay (RB), Paradise Cay (PC), Strawberry Channel (SC), Loch Lomond (LL), and Yacht Harbor 

(YH)—in San Francisco Bay, California.—Continued

[In some cases, we identified to broader taxa (such as family) when pieces of organisms were encountered or when organisms were too small for distinguishing 

identifying features. Broader taxonomic categories are not included in total taxa count if they were represented by lower taxonomic identification (ID)]

Broad taxonomic group Lowest taxonomic ID Taxonomic 

rank

MR RB PC SC LL YH

D U D U D U D U D U D U

Sabaco elongatus Species X X X X X X

Spionidae Family X

Sipuncula Sipuncula Phylum X X X X

Tanaidacea Tanaidacea Order X

Unknown Unknown X X X X X X X X X X X X

Total taxa observed 12 9 17 18 8 14 11 15 9 7 9 16
Figure 24. Mean densities (individuals/ square meter [m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa in dredged and undredged areas aRoad, Pier 32, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay. Cores were collected at Piestudy (November 2015); at Mooring Road, Richardson Bay, Paradise Cay, and Strawberry Channel during the pilot and full studies (November 2015, AuAugust 2017); and at Loch Lomond and Yacht Harbor during the full study (August 2016, January 2017, August 2017).
Figure 25. Mean biomass (grams per square meter [g/m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa in dredged and undredged areas aRichardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay. Cores were collected at all sites during thJanuary 2017, August 2017).
Figure 26. Mean energy (kilojoule per square meter [kJ/m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa in dredged and undredged areas Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay. Cores were collected at all sites during thJanuary 2017, August 2017).
44 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Yacht Harbor had the greatest average macroinvertebrate 

density out of all the undredged areas at sites 

(9,600 individuals/m2); this was 113 percent greater than the 

density in the dredged area (4,501 individuals/m2; table 9). 

Table 9. Comparison of mean (± standard error) macroinvertebrate density (number of individuals/square meter [m2]), biomass 

(grams [g]/m2) in dry weight (dw), and energy (kilojoules per square meter [kJ/m2]) in dredged and undredged areas during the pilot 

and full study in each site.

[The number of cores taken at each site during each sampling period is given (N)]

Site

Dredged Undredged

N Mean density 

(individuals/m2)

Mean biomass 

(g/m2 dw)

Mean energy 

(kJ/m2) N Mean density (individuals/m2)

Mean biomass 

(g/m2 dw)

Mean energy 

(kJ/m2)

November 2015 (Pilot)

Pier 32 12 6247.4 ± 1331.4 — 18 5208.8 ± 881.6 —

Mooring Road 7 1164.7 ± 389.6 — 12 1321.7 ± 451.6 —

Richardson Bay 20 2818.5 ± 559.6 — 13 7520.9 ± 1903.7 —

Paradise Cay 24 5146.0 ± 1235.7 — 21 8135.3 ± 901.9 —

Strawberry Channel 17 1502.5 ± 497.7 — 22 1757.4 ± 356.2 —

August 2016

Mooring Road 7 6475.6 ± 597.8 559.49 ± 62.45 1791.5 ± 199.2 12 8929.0 ± 920.9 551.57 ± 101.57 1828.4 ± 327.8

Richardson Bay 10 4526.6 ± 671.5 12.26 ± 2.89 187.4 ± 49.6 22 8661.3 ± 2665.6 17.12 ± 3.22 251.4 ± 41.3

Paradise Cay 24 4995.1 ± 935.5 0.57 ± 0.11 8.5 ± 1.3 21 1658.3 ± 449.0 6.82 ± 2.08 90.1 ± 20.3

Strawberry Channel 17 3115.8 ± 729.3 5.84 ± 3.87 42.2 ± 16.6 22 2743.4 ± 423.8 2.75 ± 0.33 46.7 ± 5.5

Loch Lomond 28 1337.0 ± 178.5 3.92 ± 1.75 20.7 ± 6.9 20 5838.1 ± 897.5 27.38 ± 4.58 392.0 ± 66.3

Yacht Harbor 22 3828.6 ± 604.3 1.14 ± 0.33 11.1 ± 2.0 21 8858.5 ± 862.3 6.75 ± 1.44 83.8 ± 18.2

January 2017

Mooring Road 7 3046.8 ± 258.2 296.67 ± 4.34 959.5 ± 138.9 12 4552.0 ± 979.6 286.32 ± 69.15 945.4 ± 224.2

Richardson Bay 10 9498.8 ± 1758.1 1.92 ± 0.32 30.1 ± 5.1 22 5209.0 ± 1246.8 28.72 ± 5.15 452.9 ± 79.7

Paradise Cay 24 11085.7 ± 

1319.6

1.06 ± 0.14 13.9 ± 1.5 21 2740.6 ± 344.5 4.17 ± 0.76 62.8 ± 12.4

Strawberry Channel 17 2864.9 ± 702.8 2.22 ± 1.22 14.8 ± 4.5 22 11129.8 ± 

1042.6

14.39 ± 2.15 241.9 ± 35.5

Loch Lomond 28 1502.9 ± 525.6 0.50 ± 0.10 8.0 ± 1.7 20 4386.5 ± 826.8 35.20 ± 12.12 580.4 ± 200.9

Yacht Harbor 22 4829.9 ± 688.0 0.81 ± 0.17 10.4 ± 1.9 21 6994.1 ± 1444.9 1.53 ± 0.51 17.4 ± 7.9

August 2017

Mooring Road 7 645.7 ± 98.7 52.16 ± 24.18 179.9 ± 76.6 12 1299.8 ± 192.8 36.69 ± 8.07 123.8 ± 25.8

Richardson Bay 10 2482.9 ± 659.6 27.82 ± 12.51 122.6 ± 43.9 22 7228.9 ± 1567.9 48.39 ± 9.16 203.5 ± 32.6

Paradise Cay 24 9775.2 ± 999.2 38.39 ± 5.72 516.0 ± 91.0 21 5987.5 ± 516.5 30.45 ± 6.52 208.2 ± 51.6

Strawberry Channel 17 2629.0 ± 466.6 78.48 ± 15.26 263.5 ± 50.0 22 8432.7 ± 801.8 75.81 ± 17.62 278.9 ± 56.3

Loch Lomond 28 2342.0 ± 269.6 47.28 ± 8.73 191.1 ± 31.0 20 6315.6 ± 959.9 77.55 ± 6.92 265.0 ± 22.1

Yacht Harbor 22 4844.3 ± 615.8 6.14 ± 2.08 53.4 ± 9.5 21 12948.3 ± 

1033.5

81.33 ± 15.91 384.8 ± 63.5

All Sampling Periods

Mooring Road 28 2878.57 ± 477.2 302.77 ± 52.7 977.0 ± 167.7 48 4012.22 ± 569.9 291.53 ± 53.4 965.9 ± 174.4

Richardson Bay 40 5105.93 ± 686.8 14.00 ± 4.6 113.3 ± 24.5 88 6594.40 ± 910.0 31.41 ± 3.9 302.6 ± 34.1

Paradise Cay 96 8329.50 ± 713.6 13.34 ± 2.8 179.5 ± 41.1 81 4416.47 ± 396.2 13.81 ± 2.7 120.4 ± 20.2

Strawberry Channel 67 2554.20 ± 298.2 28.85 ± 7.2 106.9 ± 23.3 88 6017.07 ± 545.4 30.98 ± 7.1 189.2 ± 25.3

Loch Lomond 84 1727.29 ± 208.9 17.23 ± 3.7 73.3 ± 13.9 60 5513.39 ± 519.8 46.71 ± 5.6 412.5 ± 71.7

Yacht Harbor 66 4500.92 ± 366.9 2.70 ± 0.8 25.0 ± 4.0 63 9600.28 ± 718.8 29.87 ± 7.0 162.0 ± 29.8
Results 45

In the dredged area, polychaetes were the most abundant 

taxa (36 percent), followed by amphipods (24 percent) and 

oligochaetes (18 percent). In the undredged area, amphipods 

were the most abundant taxa, followed by cumaceans 

(21 percent) and polychaetes (15 percent). Biomass in the 

dredged area at Yacht Harbor was the lowest among all the 

sites (2.7 g/m2 dw), while the biomass in the undredged area 

was 1007 percent greater (29.9 g/m2 dw; table 9). Bivalves 

and polychaetes contributed the most biomass in both dredged 

(53 percent and 37 percent, respectively) and undredged areas 

(83 percent and 10 percent, respectively). Energy content 

was 548 percent greater in the undredged area compared to 

the dredged, and unlike other sites, this was driven mainly by 

bivalves (49 percent of total energy; fig. 26).

The Effect of Dredging on Macroinvertebrate 

Density, Biomass, and Energy Content

Total density of macroinvertebrate taxa was significantly 

greater in undredged areas compared to dredged areas for 

all size classes and depths (table 10). Macroinvertebrate 

density increased as salinity increased, decreased as elevation 

increased, and was greater during the winter than during the 

summer (table 10). The taxonomic composition of the benthic 

community differed among sampling periods with Polychaeta 

found in greatest densities during the November 2015 

and January 2017 sampling periods, Nematoda found in 

the greatest densities during the August 2016 sampling 

period, and Amphipoda found in greatest densities during 

the August 2017 sampling period (fig. 27–30). Overall, the 

number of broad taxa and macroinvertebrate densities were 

much greater in shallow core fractions (0–4 cm) compared to 

deeper core fractions (4–10 cm; figs. 31–32). Polychaeta with 

a 0–4 mm head width was the most abundant taxon in shallow 

cores (fig. 31).

Total biomass of macroinvertebrate prey of all sizes 

(0–50 mm) in both surface (0–4 cm) and whole cores 

(0–10 cm) was consistently greater in undredged areas 

compared to dredged areas (table 11). We did not detect 

any clear effects of season, salinity, or elevation on 

biomass; the effects varied depending on the core depth and 

macroinvertebrate size class (table 11). Biomass of 0–50 mm 

macroinvertebrates in whole cores (0–10 cm) varied among 

sampling periods. Biomass was much greater at Mooring 

Road compared to all other sites during the August 2016 

sampling period, and it was much greater at Richardson Bay 

compared to all other sites during the January 2017 sampling 

period (figs. 33–34). Biomass was more similar among sites 

during the August 2017 sampling period (fig. 35). At all sites, 

most of the available biomass was from Bivalvia followed 

by Polychaeta and was found near the surface (0–4 cm deep; 

figs. 36–37). Bivalvia biomass was particularly high at 

Mooring Road during August 2016 and at Richardson Bay 

during January 2017 (figs. 33–34). Bivalvia near the surface 

(0–4 cm deep) in the 12–24 mm size class represented the 

greatest biomass at each site, followed by 4–12 mm and 

24–50 mm Bivalvia near the surface and 12–24 mm Bivalvia 

in deeper sediments (4–10 cm deep; figs. 36–37). Polychaeta 

(0–4 mm head width) represented the taxa with the second 

greatest biomass in deeper sediments (fig. 37).

Table 10. Summary of general linear mixed model (GLMM) 

results for total density of macroinvertebrates from different 

size classes found in shallow (0–4 centimeters [cm]) and deep 

(0–10 cm) cores at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and Yacht 

Harbor) with dredged and undredged areas.

[Cores were collected during August 2016, January 2017, and August 2017. 

Collection site and transects were included in the GLMM as random 

effects. Orange indicates the relationship between density and the fixed 

effect was positive, and purple indicates that the relationship was negative. 

See full GLMM tables 1.1 to 1.5 in appendix for more information. 

Abbreviations: mm, millimeter; >, greater than; <, less than]

Core depth 0–4 cm 0-10 cm

Macroinvertebrate 

size class

0–4

mm

>4–12 

mm

>12–24 

mm

>24–50 

mm

0–50 mm

Fixed effect p p p p p

Intercept <0.001 <0.001 <0.001 0.490 <0.001

Treatment: 

undredged

<0.001 <0.001 <0.001 0.002 <0.001

Season: winter <0.001 <0.001 0.005 0.484 0.024

Salinity <0.001 <0.001 0.120 0.507 0.023

Elevation <0.001 <0.001 0.019 0.271 <0.001

Table 11. Summary of general linear mixed model (GLMM) 

results for total biomass of macroinvertebrates from different 

size classes found in shallow (0–4 centimeters [cm]) and deep 

(0–10 cm) cores at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and Yacht 

Harbor) within dredged and undredged areas.

[Cores were collected during summer and winter 2016–17. Collection site and 

transects were included in the GLMM as random effects. Orange indicates 

the relationship between density and the fixed effect was positive, and purple 

indicates that the relationship was negative. See full GLMM tables 1.7 to 1.11 

in appendix for more information. Abbreviations: mm, millimeter; >, greater 

than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class

0–4

mm

>4–12 

mm

>12–24 

mm

>24–50 

mm

0–50 mm

Fixed effect p p p p p

Intercept <0.001 <0.001 <0.001 <0.001 <0.001

Treatment: 

undredged

<0.001 <0.001 0.036 0.169 <0.001

Season: winter <0.001 <0.001 0.006 <0.001 <0.001

Salinity <0.001 <0.001 0.112 <0.001 0.012

Elevation 0.003 0.417 0.002 <0.001 0.002
Figure 27. Mean densities (individuals/meter [m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredged and undredged areas (Pier 32, Mooring Road, Richardson Bay, Paradise Cay, and Strawberry Channel) in November 2015.
Figure 28. Mean densities (individuals/meter [m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredged and undredged areas Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in August 2016.
Figure 29. Mean densities (individuals/ meter [m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredged and undredged areas (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in January 2017.
Figure 30. Mean densities (individuals/ meter [m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredged and undredged areas (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in August 2017.
Figure 31. Mean density (individuals/ meter [m2]) of macroinvertebrate taxa from different size classes in shallow cores (0–4 centimeter [cm]) from dareas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay. CoMooring Road, Richardson Bay, Paradise Cay, and Strawberry Channel during the pilot and full studies (November 2015, August 2016, January 2017, ALomond and Yacht Harbor during the full study (August 2016, January 2017, August 2017).
Figure 32. Mean density (individuals/meter [m2]) of macroinvertebrate taxa from different size classes in deep cores (4–10 centimeter [cm]) from dreareas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Francisco Bay. CoMooring Road, Richardson Bay, Paradise Cay, and Strawberry Channel during the pilot and full studies (November 2015, August 2016, January 2017, ALomond and Yacht Harbor during the full study (August 2016, January 2017, August 2017).
Figure 33. Mean biomass (grams per square meter [g/m2] dry weight (dw) to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredgsix study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in August 2016.
Figure 34. Mean biomass (grams per square meter [g/m2] dry weight (dw) to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredgsix study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in January 2017.
Figure 35. Mean biomass (grams per square meter [g/m2] dry weight (dw) to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredg

six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in August 2017.
Figure 36. Mean biomass grams per square meter [g/m2] dry weight (dw) of macroinvertebrate taxa from different size classes in shallow cores (0–4 dredged and undredged areas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) Cores were collected at all sites during the full study (August 2016, January 2017, August 2017).
Figure 37. Mean biomass (grams per square meter [g/m2] dry weight (dw) of macroinvertebrate taxa from different size classes in deep cores (4–10 dredged and undredged areas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) Cores were collected at all sites during the full study (August 2016, January 2017, August 2017).
Results 57

Total energy content of 0–4 mm and 4–12 mm 

macroinvertebrate prey in surface cores (0–4 cm) and 

0–50 mm prey in whole cores (0–10 cm) was significantly 

greater in undredged areas compared to dredged areas 

(table 12). As with biomass, there were no clear effects of 

season, salinity, or elevation on energy content; instead, 

the effects varied depending on the core depth and 

macroinvertebrate size class (table 12). Overall, energy 

content of all macroinvertebrate size classes (0–50 mm) in 

whole cores (0–10 cm) varied among sampling periods. In 

August 2016 and January 2017, energy content was much 

greater at dredged and undredged locations at Mooring Road 

(dominated by Bivalvia) compared with all other sites that 

were dominated by Polychaeta (fig. 38, 39). Energy content 

was more similar among sites during the August 2017 

sampling period, though Paradise Cay dredged area notably 

had the greatest energy content and was dominated by 

Polychaeta (fig. 40). In contrast to biomass, much of the 

available energy content at each site for both surface and deep 

cores was from Polychaeta, except for Mooring Road which 

was dominated by energy from Bivalvia near the surface 

(0–4 cm deep) in the 12–24 mm size class (figs. 41–42).

Overall, potential trophic support for target fishes 

expressed as average prey biomass available for each species 

and age class across all sampling sites ranged from 3.04 g/m2

for juveniles fishes that forage on 0–4 mm prey in the shallow 

(0–4 cm) sediment of dredged areas to 56.97 g/m2 for larger 

fishes exploiting prey in all size classes (0–50 mm) in both 

shallow and deep (0–10 cm) sediment in undredged areas 

(table 2). Total mean available prey biomass in dredged sites 

range from 35 to 51 percent less than that in undredged sites 

(table 2). Average energy (secondary productivity) ranged 

from a low of 50.23 kJ/m2 for 0–4 mm prey in shallow, 

dredged sediments to a high of 310.11 kJ/m2 for fish that 

consume all prey size classes at all core depths (table 2). Total 

mean available energy was 40 to 50 percent less at dredged 

sites compared to undredged sites (table 2).

Table 12. Summary of general linear mixed model (GLMM) 

results for total energy of macroinvertebrates from different 

size classes found in shallow (0–4 centimeters [cm]) and deep 

(0–10 cm) cores at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and Yacht 

Harbor) within dredged and undredged areas.

[Cores were collected during summer and winter 2016–17. Collection site and 

transects were included in the GLMM as random effects. Orange indicates 

the relationship between density and the fixed effect was positive, and purple 

indicates that the relationship was negative. See full GLMM tables 1.12 to 

1.16 in appendix for more information. Abbreviations: mm, millimeter; 

>, greater than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class

0–4 

mm

>4–12 

mm

>12–24 

mm

>24–50 

mm

0–50 

mm

Fixed effect p p p p p

Intercept <0.001 <0.001 <0.001 <0.001 <0.001

Treatment: 

undredged

<0.001 <0.001 0.467 0.249 <0.001

Season: winter <0.001 <0.001 0.952 <0.001 0.016

Salinity <0.001 0.002 0.408 <0.001 0.001

Elevation 0.004 0.087 0.001 <0.001 0.794
Figure 38. Mean energy (kilojoules per square meter [kJ/m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredged and undresites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in August 2016.
Figure 39. Mean energy (kilojoules per square meter [kJ/m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredged and undresites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in January 2017.
Figure 40. Mean energy (kilojoules per square meter [kJ/m2] to 10 centimeter [cm] depth) of macroinvertebrate taxa collected in dredged and undresites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in August 2017.
Figure 41. Mean energy (kilojoules per square meter [kJ/m2]) of macroinvertebrate taxa from different size classes in shallow cores (0–4 centimeter undredged areas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Franccollected at all sites during the full study (August 2016, January 2017, August 2017).
Figure 42. Mean energy (kilojoules per square meter [kJ/m2]) of macroinvertebrate taxa from different size classes in deep cores (4–10 centimeter [cundredged areas at six study sites (Mooring Road, Richardson Bay, Paradise Cay, Strawberry Channel, Loch Lomond, and Yacht Harbor) in San Franccollected at all sites during the full study (August 2016, January 2017, August 2017).
Results 63

The Effect of Distance and Time on 

Macroinvertebrate Density, Biomass and 

Energy Content

The effect of distance to nearest dredged area on 

macroinvertebrate density, biomass, and energy differed 

among macroinvertebrate size classes and core depths. 

Density of 0–4 mm macroinvertebrates at the surface 

(0–4 cm deep) decreased significantly with increasing 

distance from dredged area, while densities of all other size 

classes and core depths, except for 24–50 mm size-class at 

the surface were not significantly affected by the distance to 

nearest dredged area (table 13; fig. 43). Likewise, biomass 

of 0–4 mm macroinvertebrates at the surface (0–4 cm 

deep) also decreased significantly as distance to the nearest 

dredged area increased; however, biomass of 12–24 mm 

and 24–50 mm macroinvertebrate size classes at the surface 

and 0–50 mm macroinvertebrates in whole cores (0–10 cm 

deep) increased significantly as the distance to the nearest 

dredged area increased (table 14; fig. 44). Energy content of 

0–4 mm surface (0–4 cm deep) macroinvertebrates followed 

the same patterns as density and biomass, decreasing 

significantly as distance to the nearest dredged area increased. 

Similar to biomass, energy content of 12–24 mm and 

24–50 mm macroinvertebrates at the surface and 0–50 mm 

macroinvertebrates in whole cores (0–10 cm deep) increased 

significantly as the distance to the nearest dredged area 

increased (table 15; fig. 45).

We found a positive effect of time-since-dredging on 

macroinvertebrate density, biomass, and energy content. All 

three parameters increased significantly for all size classes 

and core depths as time-since-dredging increased, except 

for the density of 0–4 mm macroinvertebrates at the surface 

which was not significantly affected by time-since-dredging 

(tables 16–18; figs. 46–48). In addition, density, biomass, 

and energy models for 24–50 mm macroinvertebrates in 

surface cores did not converge, so an effect of time could 

not be evaluated for this class of macroinvertebrates. Season 

(winter) and salinity had a negative relationship with 

biomass and energy content for all size classes and core 

depths (tables 17–18).

Table 13. Summary of general linear mixed model (GLMM) 

results testing the effects of distance from dredged areas 

(meters [m]), season, salinity (practical salinity units [psu]), 

and elevation (m) on total density of macroinvertebrates from 

different size classes found in shallow (0–4 centimeters [cm]) 

and deep (0–10 cm) cores at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during August 2016, January 2017, and August 2017. 

Collection site and transects were included in the GLMM as random 

effects. Orange indicates the relationship between density and the fixed 

effect was positive, and purple indicates that the relationship was negative. 

See full GLMM tables 1.17 to 1.21 in appendix for more information. 

Abbreviations: mm, millimeter; >, greater than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class

0–4

mm

>4–12 

mm

>12–24 

mm

>24–50 

mm

0–50 mm

Fixed effect p p p p p

Intercept <0.001 <0.001 <0.001 X1 <0.001

Distance from 

dredged (m) 0.043 <0.001 <0.001 0.423

Season: winter <0.001 <0.001 0.006 0.018

Salinity <0.001 <0.001 0.133 0.013

Elevation <0.001 <0.001 0.235 <0.001

1Model did not converge owing to limited data.

Table 14. Summary of general linear mixed model (GLMM) 

results testing the effects of distance to nearest dredged areas 

(meters [m]), season, salinity (practical salinity units [psu]), 

and elevation (m) on total biomass of macroinvertebrates from 

different size classes found in shallow (0–4 centimeters [cm]) 

and deep (0–10 cm) cores at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection site and 

transects were included in the GLMM as random effects. Orange indicates 

the relationship between density and the fixed effect was positive, and purple 

indicates that the relationship was negative. See full GLMM tables 1.22 to 

1.26 in appendix for more information. Abbreviations: mm, millimeter; 

>, greater than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class 0–4 mm >4–12 mm

>12–24 

mm

>24–50 

mm

0–50 mm

Fixed effect P p p p p

Intercept 0.004 <0.001 <0.001 <0.001 <0.001

Distance from 

dredged (m) 0.038 0.134 0.419 0.605 <0.001

Season: winter <0.001 <0.001 0.005 <0.001 <0.001

Salinity <0.001 <0.001 0.110 <0.001 0.053

Elevation 0.355 0.147 <0.001 <0.001 <0.001
> > > Figure 43. Change in macroinvertebrate density (individuals/square meter [m2]) by size class in shallow (0–4 centimeter [cm]) and whole (0–10 cm) c

increasing distance (meter [m]) from a dredged area. Cores were collected at six study sites (Loch Lomond, Mooring Road, Paradise Cay, Richardson and Yacht Harbor) in San Francisco Bay.
>

> >

Figure 44. Change in macroinvertebrate biomass (grams per square meter dry weight [g/m2 dw]) by size class in shallow (0–4 centimeters [cm]) and fractions with increasing distance (meters [m]) from a dredged area. Cores were collected at six study sites (Loch Lomond, Mooring Road, Paradise CStrawberry Channel, and Yacht Harbor) in San Francisco Bay.
66 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 15. Summary of general linear mixed model (GLMM) 

results testing the effects of distance from dredged areas 

(meters [m]), season, salinity (practical salinity units [psu]), 

and elevation (m) on total energy of macroinvertebrates from 

different size classes found in shallow (0–4 centimeters [cm]) 

and deep (0–10 cm) cores at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection site and 

transects were included in the GLMM as random effects. Orange indicates 

the relationship between density and the fixed effect was positive, and purple 

indicates that the relationship was negative. See full GLMM tables 1.27 to 

1.31 in appendix for more information. Abbreviations: mm, millimeter; 

>, greater than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class

0–4 

mm

>4–12 

mm

>12–24 

mm

>24–50 

mm

0–50 

mm

Fixed effect p p p p p

Intercept <0.001 <0.001 <0.001 <0.001 <0.001

Distance from 

dredged (m) 0.032 0.061 0.277 0.570 <0.001

Season: winter <0.001 <0.001 0.946 <0.001 0.136

Salinity <0.001 0.003 0.415 <0.001 <0.001

Elevation 0.286 0.022 <0.001 <0.001 0.009

Table 16. Summary of general linear mixed model (GLMM) 

results testing the effects of time-since-dredged (years), season, 

salinity (practical salinity units [psu]), and elevation (meters [m]) 

on total density of macroinvertebrates from different size classes 

found in shallow (0–4 centimeter [cm]) and deep (0–10 cm) 

cores at six sites (Loch Lomond, Mooring Road, Paradise Cay, 

Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during August 2016, January 2017, and August 2017. 

Collection site and transects were included in the GLMM as random 

effects. Orange indicates the relationship between density and the fixed 

effect was positive, and purple indicates that the relationship was negative. 

See full GLMM tables 1.32 to 1.36 in appendix for more information. 

Abbreviations: mm, millimeter; >, greater than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class

0–4 

mm

>4–12 

mm

>12–24 

mm

>24–50 

mm

0–50 

mm

Fixed effect p p p p p

Intercept <0.001 <0.001 0.262 X1 <0.001

Time since dredged 

(years) 0.144 0.025 0.015 0.001

Season: winter 0.032 <0.001 0.035 0.403

Salinity 0.092 <0.001 0.868 0.551

Elevation 0.141 0.005 0.220 0.174

1Model did not converge owing to limited data.

Table 18. Summary of general linear mixed model (GLMM) 

results testing the effects of time since dredged (years), season, 

salinity (practical salinity units [psu]), and elevation (meters [m]) 

on total energy of macroinvertebrates from different size classes 

found in shallow (0–4 centimeters [cm]) and deep (0–10 cm) 

cores at six sites (Loch Lomond, Mooring Road, Paradise Cay, 

Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection site and 

transects were included in the GLMM as random effects. Orange indicates 

the relationship between density and the fixed effect was positive, and purple 

indicates that the relationship was negative. See full GLMM tables 1.41 to 

1.44 in appendix for more information. Abbreviations: mm, millimeter; >, 

greater than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class

0–4 

mm

>4–12 

mm

>12–24 

mm

>24–50 

mm

0–50 

mm

Fixed effect p p p p p

Intercept <0.001 <0.001 <0.001 X1 <0.001

Time since dredged 

(years) <0.001 <0.001 0.003 <0.001

Season: winter <0.001 <0.001 <0.001 <0.001

Salinity 0.019 <0.001 <0.001 <0.001

Elevation 0.006 0.003 0.129 0.013

1Model did not converge owing to limited data.

Table 17. Summary of general linear mixed model (GLMM) 

results testing the effects of time since dredged (years), season, 

salinity (practical salinity unit [psu]), and elevation (meter [m]) on 

total biomass of macroinvertebrates from different size classes 

found in shallow (0–4 centimeters [cm]) and deep (0–10 cm) 

cores at six sites (Loch Lomond, Mooring Road, Paradise Cay, 

Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection site and 

transects were included in the GLMM as random effects. Orange indicates 

the relationship between density and the fixed effect was positive, and purple 

indicates that the relationship was negative. See full GLMM tables 1.37 to 

1.40 in appendix for more information. Abbreviations: mm, millimeter; 

>, greater than; <, less than]

Core depth 0–4 cm 0–10 cm

Macroinvertebrate 

size class 0–4 mm >4–12 mm

>12–24 

mm

>24–50 

mm

0–50 mm

Fixed effect p p p P p

Intercept 0.177 <0.001 <0.001 X1 <0.001

Time since dredged 

(years) <0.001 <0.001 0.025 <0.001

Season: winter <0.001 <0.001 <0.001 <0.001

Salinity 0.032 <0.001 <0.001 <0.001

Elevation 0.003 0.059 0.167 0.414

1Model did not converge owing to limited data.
>

> >

Figure 45. Change in macroinvertebrate energy (kilojoules per square meter [kJ/m2]) by size class in shallow (0–4 centimeter [cm]) and whole (0–10 increasing distance (m) from a dredged area. Cores were collected at six study sites (Loch Lomond, Mooring Road, Paradise Cay, Richardson Bay, StrYacht Harbor) in San Francisco Bay.
> > > Figure 46. Change in macroinvertebrate density (individuals/square meter [m2]) by size class in shallow (0–4 centimeter [cm]) and whole (0–10 cm) c

increasing time (years) since a site was dredged. Cores were collected at six study sites (Loch Lomond, Mooring Road, Paradise Cay, Richardson BayYacht Harbor) in San Francisco Bay.
>

> >

Figure 47. Change in macroinvertebrate biomass (grams per square meter dry weight [g/m2 dw]) by size class in shallow (0–4 centimeters [cm]) and core fractions with increasing time (years) since a site was dredged. Cores were collected at six study sites (Loch Lomond, Mooring Road, Paradise CStrawberry Channel, and Yacht Harbor) in San Francisco Bay.
> > > Figure 48. Change in macroinvertebrate energy (kilojoules per square meter [kJ/m2]) by size class in shallow (0–4 centimeters [cm]) and whole (0–10 

increasing time (years) since a site was dredged. Cores were collected at six study sites (Loch Lomond, Mooring Road, Paradise Cay, Richardson BayYacht Harbor) in San Francisco Bay.
Discussion 71

Discussion

We evaluated the effects of maintenance dredging in 

shallow marinas on trophic support for target benthic foraging 

fish species that inhabit EFH in SFB. We used a MBRAT to 

evaluate foraging habitat quality in terms of prey availability 

for target fish species. We found significantly lower density, 

biomass, and energy content for all available prey size classes 

and depths in dredged compared to adjacent undredged areas; 

dredged areas had lower prey availability than undredged 

areas for all target fish species. However, our study also 

demonstrated significant increases in prey density, biomass, 

and energy as time since dredging increased, indicating 

functional recovery of dredged areas for benthic foraging 

fishes may begin within the 3-year window that we examined 

in this study. Distance to dredged area also influenced biomass 

and energy content of some sizes of macroinvertebrate prey, 

such that they increased significantly as distance from dredged 

area increased.

Given the scope of our study, we mainly focused on 

functional (biomass and energy content) metrics to compare 

macroinvertebrate prey availability for focal fish species as 

a function of dredging status (dredged versus undredged), 

distance to dredged areas, and time-since-dredging. The 

MBRAT method we used is a functional metric that integrated 

size class, vertical distribution in the sediment, biomass, and 

secondary productivity (energy content) to detect changes 

in prey resources as a response to dredging disturbance. 

While we did evaluate some structural measures (density 

and community taxonomic structure), our study was mainly 

focused on trophic support for target fish species, and thus our 

results were not intended to compare structural and functional 

recovery. Functional recovery of a site can occur before 

the structural recovery of a macroinvertebrate community 

(Cooper and others, 2008), and in fact there may be no clear 

relationship between the two. For example, in a study of 

14 dredge disposal sites in England, Bolam (2012) did not 

find a relationship between multivariate structural changes 

and taxonomic contribution to total energy production, 

demonstrating change in structure does not always signify 

a significant functional impact or vice versa. Functional 

traits, such as those we measured (available biomass and 

energy), have been advocated for assessing anthropogenic 

effects (Elliott and Quintino, 2007) as well as implications of 

dredging activities for foraging predators in mudflats (Lunz 

and Kendall, 1982; Bolam, 2014).

Influence of Physical Characteristics

We deliberately selected sampling sites for this study to 

minimize differences among them, such that inference about 

the effects of dredging could be maximized. Criteria for site 

selection required that physical characteristics such as salinity, 

sediment composition, and depth be within a narrow range 

among sites. However, localized seasonal influences, such as 

freshwater input from creeks, can influence site characteristics. 

The fact that we did find significant differences in some 

physical factors among sites emphasizes the importance of the 

localized, undredged reference areas included at each of our 

sampling sites to account for effects and variations that could 

not be completely accounted for across our sites, despite their 

proximity to one another. 

Consistent with other studies (Boyd and others, 2005; 

Applied Marine Sciences Inc., 2009; Abdul Wahab and 

others, 2017), we found significant differences in sediment 

characteristics between dredged and undredged sites. Although 

overall, sediments from all dredged and undredged areas were 

characterized as loamy, we found that mean percent silt was 

significantly greater in undredged sediments and sand was 

greater in dredged sites. Benthic community assemblages 

can respond to differences in sediment type and particle size 

(Desprez, 2000; Wilber and Clarke, 2007). Fine-grained silty 

sediments typically have greater macroinvertebrate density 

and taxonomic richness (Thompson and others, 2000; Lee 

and others, 2003) compared to coarser sandy sediments 

(Thompson and others, 2007). Although our study was not 

designed to evaluate the role of subtle differences in sediment 

texture on species composition, such underlying characteristics 

may have contributed to the differences we measured among 

macroinvertebrate densities and biomass between dredged and 

undredged sites.

We measured a marked decrease in demersal salinity at 

all sites during the January 2017 sampling period compared 

with all other sampling periods, including the previous winter. 

Decreased salinity coincided with anomalous extreme rainfall 

and freshwater inputs to SFB (https://nwis.waterdata.usgs.gov; 

Swain and others, 2018) as a result of multiple large-scale 

storms during winter 2016–17. During our subsequent 

sampling period (August 2017), we observed broad taxonomic 

shifts in both dredged and undredged areas at all sites, 

including sharp decreases in polychaete, oligochaete, and 

bivalve densities and large increases in amphipod densities. 

While seasonal variation in the distribution and abundance 

of benthic communities in SFB is predominantly driven by 

annual salinity cycles, inter-annual variation, such as that seen 

our study, is largely influenced by Sacramento -San Joaquin 

River Delta outflow, local runoff, or pollution (Nichols and 

Pamatmat, 1988). Similar patterns have been observed in other 

estuaries. For example, In the Mondego estuary, Portugal, 

Grilo and others (2011) found prolonged flooding had a much 

stronger negative effect on macroinvertebrate abundance than 

drought in both mudflat and sandflat environments. Similar to 

our results, deposit and suspension feeding detritivores, such 

as bivalves and oligochaetes, showed the greatest decreases in 

abundance following prolonged freshwater inputs (Grilo and 

others, 2011).
72 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Several benthic macroinvertebrate sub-assemblages 

within SFB exhibit strong responses to annual variability in 

freshwater influx (Markmann, 1986; Peterson and Vayssieres, 

2010), but Central Bay assemblages typically remain 

consistent. The Central Bay sustains a more diverse benthic 

community across seasons because the salinity regime is 

relatively stable and not as influenced by freshwater flows 

compared with other SFB regions (Thompson and others, 

2000). In winter, during increased freshwater input, the surface 

salinity in the Central Bay can rapidly decrease (from 30 to 

10 ppt); however, salinity values in demersal waters tend to be 

more stable owing to density-driven stratification (Cloern and 

others, 2000). Still, large freshwater influx to the Central Bay 

can drive spatial patterns in benthic assemblages, particularly 

in shallow shoal areas (Thompson and others, 2007). For 

example, Thompson and others (2000) found that abundance 

of the amphipod M. acherusicum in the Central Bay varied 

substantially among years and peaked in association with 

increased freshwater inputs. This is similar to the response 

we detected in amphipod abundances at all sites in summer 

2017 following the intense flooding events of winter 2016–17. 

Although we observed dramatic shifts in taxa following 

these freshwater events at all but one site (Paradise Cay), 

the number of taxa and overall densities still were greater in 

undredged compared to dredged areas the following summer.

The Effect of Dredging on Trophic Support for 

Target Fishes

Based on an extensive literature review (De La Cruz 

and others, 2016), we expected the greatest levels of trophic 

support to co-occur with peak summer densities among most 

target fishes in SFB. Although many studies have noted that 

density and biomass for some common fish prey taxa such 

as amphipods (Chapman, 1988; Cohen and Carlton, 1995; 

Greenstein and Tiefenthaler, 2013) and bivalves (Radtke, 

1966; McKechnie and Fenner, 1971; Haderlie and Abbott, 

1980; Emmett and others, 1991; Thompson and others, 2007) 

are higher during summer compared to winter months, we 

observed temporal variations in macroinvertebrate patterns 

that were independent of dredging status and were more likely 

driven by anomalous freshwater events (see discussion of 

physical characteristics above).

Similar to other studies (Hirsch and others, 1978; LaSalle, 

1990; Clarke and others, 2000; Dernie and others, 2003; 

Wilber and others, 2008; Lebednik, 2004; Rich, 2010), we 

found dredged areas had significantly less macroinvertebrate 

density, biomass, and energy content compared to paired 

undredged areas, resulting in lower overall trophic support for 

target fish species. However, the degree of impact depended 

on the macroinvertebrate size class consumed and the foraging 

depth of each target fish species. For example, juvenile Pacific 

sardine, longfin smelt, northern anchovy, and brown rockfish 

that consume the smallest prey size class (0–4 mm) and forage 

within the shallow benthos (0–4 cm depth) had the lowest 

mean prey biomass and energy available compared with all 

other target species and age classes. Both available biomass 

and energy were 44 percent less in dredged areas compared 

to undredged areas that were accessible to these fishes. 

Larger fishes and adult life stages that were able to exploit 

all macroinvertebrate size classes and both shallow and deep 

depths had more prey available to them at dredged sites, but 

this still represented an average of 41 percent less biomass and 

50 percent less energy than at undredged sites. Interestingly, 

the greatest reduction (51 percent) of available mean biomass 

in dredged areas occurred for fish that forage on the smallest 

two size classes of macroinvertebrates (0–4 and 4–12 mm) 

in shallow sediments, such as juvenile English sole and 

juvenile starry flounder. Fish species that were least impacted 

by dredging (35 percent reduction in biomass and 40 percent 

reduction in energy compared to undredged) included those 

that forage on small and intermediate size classes (0–4, 4–12, 

and 12–24 mm) in shallow sediments, such as adult Pacific 

sardine and adult longfin smelt.

As expected, based on our pilot work and previous 

studies (Clarke, 1986), we found that macroinvertebrate 

densities and biomass were concentrated in the top 0–4 cm 

of cores in both dredged and undredged areas, though in 

many undredged areas a large proportion of the total biomass 

occurred in deeper fractions of the core. Concentration 

of prey at the surface often occurs in the early stages of 

succession post dredging and in some cases can increase prey 

availability for fish species (Rhoads and Germano, 1986). 

Later successional stage macroinvertebrates are typically 

larger, longer-lived species that can burrow deeper in the 

sediment (Rhoads and Germano, 1986). For example, we 

found most of the biomass and energy in whole cores from 

undredged areas was contributed by intermediate 12–24 mm 

bivalves or 0–4 mm (head width) polychaetes. Although fewer 

in number, intermediate to large-sized (12–24 and 24–50) 

macroinvertebrates can be important, high-caloric prey for 

deep, benthic-foraging, target fishes such as leopard shark, 

Dungeness crab, sturgeon, and skates (Talent, 1976; Barry, 

1983; Barry and others, 1996; Adams and others, 2002; Ebert 

and Ebert, 2005; Yang, 2007; Bizzarro and others, 2007; 

Israel and Klimley, 2008; De La Cruz and others, 2016). 

In fact, across all undredged areas and time periods, deep 

core fractions provided up to 15 percent more available prey 

biomass and energy for species that could access this depth 

than the maximum biomass and energy contained in shallow 

core fractions from undredged areas.
Discussion 73

The of Effects of Distance and Time

We found that macroinvertebrate density, biomass, and 

energy varied by distance from a dredged area. The density 

of the smallest macroinvertebrate size class (0–4 mm) at the 

surface (0–4 cm deep) decreased significantly the farther we 

sampled from a dredged area, and biomass and energy content 

of larger size classes at deeper depths increased with distance 

from dredged area. For small-scale disturbances that result 

in the localized removal of macroinvertebrates in adjacent 

areas, one way to evaluate the effect of a dredging operation 

is to evaluate the dispersal capacity of colonizing organisms 

(Günther, 1992). Organisms with prolonged larval periods that 

include a pelagic stage, such as crab and bivalve species, may 

have a relatively greater capacity for longer‐distance dispersal 

and recolonization compared to macroinvertebrate taxa with 

crawling or brooding larvae, such as many polychaete species, 

that may disperse as juveniles or adults (Lundquist and others, 

2004). Günther (1992) found that localized disturbances were 

associated with the dispersal and recolonization by post-larval 

life stages and to a lesser degree immigration of adults, 

whereas in larger disturbed sites, recovery was predominately 

from the dispersal of long-distance planktonic larvae. 

Lundquist and others (2004) conducted simulations with a 

hydrodynamic and particle-tracking model and predicted that 

small larvae would disperse farther than larger, heavier larvae 

and juveniles. At our sites, the greatest densities and biomass 

of the smallest macroinvertebrate species were found closer to 

dredged areas, while larger species increased with increasing 

distance from the dredge area, indicating maintenance 

dredging may have created localized disturbance that impacted 

the size class, depth, biomass, and energy content of adjacent 

benthic communities at short distances. Fishes that forage on 

the smallest prey on the sediment surface (such as, juvenile 

Pacific sardine, juvenile longfin smelt, juvenile rockfish) may 

in some cases benefit from such disturbance, while larger 

fishes that consume larger prey (0–24 mm or 0–50 mm) at the 

surface or to 10-cm depth (such as. adult northern anchovy, 

adult starry flounder, adult brown rockfish, adult California 

halibut) may experience reduced available prey resources.

By incorporating marinas that were dredged at 1, 2, 

and 3 years prior to our study, we were able to examine 

how quickly structural and functional metrics of benthic 

habitat for foraging fish might begin to approximate those of 

adjacent undredged areas. We found that macroinvertebrate 

density, biomass, and energy content within every size class 

and depth, except density of 0–4 mm prey and energy from 

12 to 24 mm prey in shallow sediments, increased with 

time-since-dredging. From the standpoint of trophic support 

for fishes, our findings indicate an increase in available prey 

coincided with time-since-dredging for most species and ages 

of target fishes. However, after repeatedly sampling the same 

sites during four sampling periods across 2 years, we found 

that overall prey density, biomass, and energy in dredged 

areas only approximated that of undredged areas at two sites, 

Mooring Road and Paradise Cay, dredged 3 and 2 years prior 

to the study’s inception. Thus, whereas a site may begin to 

be recolonized shortly after dredging, our study indicated it 

can take more than 1 to 3 years for a site to recover trophic 

functions that approximate those of adjacent undredged areas.

Defining benthic recovery and determining the time 

required for recovery remains a major challenge for the 

scientific community (Rhoads and Germano, 1986; Bolam 

and Rees, 2003; Wilber and Clarke, 2007; Wilber and others, 

2008). Recovery is often defined as the return of a dredged 

area to a baseline, pre-impact, or, like the local undredged 

areas that we evaluated in this study, some definable reference 

state. Limited information exists about benthic community 

recovery from dredge disturbance in SFB, and no previous 

SFB studies have evaluated recovery of relative foraging 

value for benthic fishes. In contrast to our study conducted 

in shallow, fine-grained sediment marinas, a sand mining 

study in deep-water channels within the Central Bay indicated 

no significant differences in number of taxa or abundance 

between control areas and areas mined within the previous 

3 years (Applied Marine Sciences Inc., 2009). Kenny and Rees 

(1994) monitored recolonization of a benthic community after 

a dredge event in the North Sea and observed similar rapid 

recolonization rates as in our study, but no notable increase in 

biomass, which in their study indicated the loss of large taxa. 

At our sites, we observed lower biomass and energy content 

among larger prey size classes in dredged areas, particularly at 

sites dredged 1 to 2 years before our study.
74 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Summary

We measured macroinvertebrate density, biomass, and 

energy content in adjacent dredged and undredged areas at 

six Central Bay shallow marinas dredged during 2013, 2014, 

or 2015 to evaluate trophic support for SFB benthic foraging 

fishes in relationship to: (1) dredged versus undredged 

locations, (2) distance to dredged areas, and (3) years since 

dredging. We found several implications for foraging target 

fish species using these habitats:

• Low salinity events in the Central Bay during winter 

2016–17 resulted in broad taxonomic shifts in both 

dredged and undredged areas at all sites, including 

sharp decreases in polychaete, oligochaete, and bivalve 

densities and large increases in amphipod densities. At 

all but one site (Paradise Cay), the number of taxa and 

overall densities were greater in undredged compared 

to dredged areas during the following summer 

sampling period.

• We detected 104 unique taxa in the shallow 

(0–4 cm) depth compared to 43 unique taxa in the 

deep (4–10 cm) depth range. We found a greater 

taxonomic richness in undredged areas compared to 

dredged areas.

• Overall, in comparison to undredged reference areas, 

dredged areas had lower trophic support for all species 

and ages of fishes included in our study.

• There appeared to be differential impacts of 

dredging on trophic support for fishes based on 

macroinvertebrate size class that can be consumed 

and the depth to which certain fish can forage. For 

example, fish species that forage on the two smallest 

size classes of macroinvertebrates (0–4 and 4–12 mm) 

in shallow benthic habitats, namely juvenile English 

sole and juvenile starry flounder, experienced the 

greatest potential impact (51 percent decline in 

available prey biomass in dredged compared to 

undredged areas). While fish that were able to exploit 

small and intermediate prey size classes (0–4, 4–12, 

and 12–24 mm) in shallow benthic habitats, such as 

adult Pacific sardine and adult longfin smelt, only 

experienced a 35 percent reduction in biomass at 

dredge compared to undredged areas.

• The impact of distance from a dredged area varied 

by prey size class. Density, biomass, and energy 

content of the smallest prey size class (0–4 mm) 

increased closest to dredge disturbance, while larger 

macroinvertebrate prey resources (12–24 mm and 

24–50 mm) had increasing biomass associated with 

increasing distance from a dredged area.

• In general, macroinvertebrate density, biomass, and 

energy content within every size class and depth, 

except density of 0–4 mm prey in shallow sediments, 

increased with time-since-dredging.

• We found a positive effect of time-since-dredging on 

macroinvertebrate density, biomass, and energy content 

such that all three increased for most size classes and 

depths over time; however, there was little evidence 

that these measures in dredged areas were equivalent to 

those of undredged areas within the one to three-year 

time window we examined.
References Cited 75

References Cited

Abdul Wahab, M.A., Fromont, J., Gomez, O., Fisher, R., 

and Jones, R., 2017, Comparisons of benthic filter feeder 

communities before and after a large-scale capital dredging 

program: Marine Pollution Bulletin, v. 122, no. 1–2, p. 

176–193, https://doi.org/10.1016/j.marpolbul.2017.06.041.

Ackerman, L.T., 1971, Contributions to the biology of the 

leopard shark, Triakis semifasciata (Girard) in Elkhorn 

Slough, Monterey Bay, California: California State 

University, Sacramento, 61 p.

Adams, P.B., Grimes, C.B., Hightower, J.E., Lindley, S.T., 

and Moser, M.L., 2002, Status review for North American 

green sturgeon, Acipenser medirostris: Santa Cruz, Calif., 

National Marine Fisheries Service, 50 p.

Allen, L.G., 1988, Recruitment, distribution, and feeding 

habits of young-of-the-year California halibut (Paralichthys 

californicus) in the vicinity of Alamitos Bay-Long Beach 

Harbor, California, 1983–1985: Bulletin of the Southern 

California Academy of Sciences, v. 87, p. 19–30.

Ambrose, D.A., 1976, The distribution, abundance, and 

feeding ecology of four species of flatfish in the vicinity 

of Elkhorn Slough, California: Thesis, San Jose State 

University, 121 p.

Applied Marine Sciences Inc, 2009, Benthic survey of 

commercial aggregate mining leases in central San 

Francisco Bay and western Delta. In, California State Lands 

Commission, Final Environmental Impact Report, San 

Francisco Bay and Delta Sand Mining Project, Appendix F: 

California State Clearninghouse, No 2007072036, 58 p., 

https://www.slc.ca.gov/ceqa/sf-delta-sand-mining. 

Barnard, P.L., Schoellhamer, D.H., Jaffe, B.E., and 

McKee, L.J., 2013, Sediment transport in the San Francisco 

Bay coastal system—An overview: Marine Geology, v. 345, 

p. 3–17, https://doi.org/10.1016/j.margeo.2013.04.005.

Barry, J.P., 1983, Utilization of shallow marsh habitats 

by fishes in Elkhorn Slough: California, San Jose State 

University, 107 p., http://islandora.mlml.calstate.edu/

islandora/object/islandora%3A461/datastream/OBJ/

download/Utilization_of_shallow_marsh_habitats_by_

fishes_in_Elkhorn_Slough__California.pdf.

Barry, J.P., Yoklavich, M.M., Cailliet, G.M., Ambrose, D.A., 

and Antrim, B.S., 1996, Trophic ecology of the dominant 

fishes in Elkhorn Slough, California, 1974–1980: Estuaries, 

v. 19, no. 1, p. 115–138, https://doi.org/10.2307/1352657.

Baxter, R., 2009, A status review of the longfin smelt 

(Spirinchus thaleichthys) in California: Department of Fish 

and Game, 131 p., https://deltarevision.com/2002_docs/

LongfinSmeltStatusReview.pdf.

Baxter, R., Hieb, K., DeLeon, S., Fleming, K., and Orsi, 

J., 1999, Report on the 1980–1995 fish, shrimp, and 

crab sampling in the San Francisco Estuary, California: 

Interagency Ecological Program for the Sacramento-San 

Joaquin Estuary, 503 p.

Bizzarro, J.J., Robinson, H.J., Rinewalt, C.S., and Ebert, D.A., 

2007, Comparative feeding ecology of four sympatric skate 

species off central California, USA: Environmental Biology 

of Fishes, v. 80, no. 2–3, p. 197–220, accessed March 24, 

2014, at https://doi.org/10.1007/s10641-007-9241-6.

Bizzarro, J.J., Yoklavich, M.M., and Wakefield, W.W., 2017, 

Diet composition and foraging ecology of U.S. Pacific Coast 

groundfishes with applications for fisheries management: 

Environmental Biology of Fishes, v. 100, no. 4, p. 375–393, 

https://doi.org/10.1007/s10641-016-0529-2.

Blaxter, J.H.S., and Hunter, J.R., 1982, The biology of 

clupeoid fishes: Advances in Marine Biology, v. 20, p. 

1–223, https://doi.org/10.1016/S0065-2881(08)60140-6.

Bogacka-Kapusta, E., Wiszniewski, G., Duda, A., 

and Kapusta, A., 2011, Feeding of hatchery-reared 

juvenile Atlantic sturgeon, Acipenser oxyrinchus 

Mitchill, released into the Drwęca River: Archives 

of Polish Fisheries, v. 19, no. 2, p. 113–117, 

https://doi.org/10.2478/v10086-011-0013-8.

Bolam, S.G., 2012, Impacts of dredged material disposal on 

macrobenthic invertebrate communities—A comparison 

of structural and functional (secondary production) 

changes at disposal sites around England and Wales: 

Marine Pollution Bulletin, v. 64, no. 10, p. 2199–2210: 

Elsevier Ltd., accessed March 20, 2014, at 

https://www.ncbi.nlm.nih.gov/pubmed/22935522.

Bolam, S.G., 2014, Macrofaunal recovery following the 

intertidal recharge of dredged material—A comparison of 

structural and functional approaches: Marine Environmental 

Research, Elsevier Ltd, v. 97 p. 15–29, accessed March 21, 

2014, at https://www.ncbi.nlm.nih.gov/pubmed/24534437.

Bolam, S.G., and Rees, H.L., 2003, Minimizing 

impacts of maintenance dredged material disposal 

in the coastal environment—A habitat approach: 

Environmental Management, v. 32, no. 2, p. 171–188, 

https://doi.org/10.1007/s00267-003-2998-2.

Bolam, S.G., Rees, H.L., Somerfield, P., Smith, R., 

Clarke, K.R., Warwick, R.M., Atkins, M., and Garnacho, 

E., 2006, Ecological consequences of dredged material 

disposal in the marine environment—A holistic assessment 

of activities around the England and Wales coastline: 

Marine Pollution Bulletin, v. 52, no. 4, p. 415–426, 

https://doi.org/10.1016/j.marpolbul.2005.09.028.
76 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Bottom, D.L., and Jones, K.K., 1990, Species 

composition, distribution, and invertebrate prey of 

fish assemblages in the Columbia River Estuary: 

Progress in Oceanography, v. 25, no. 1–4, p. 243–270, 

https://doi.org/10.1016/0079-6611(90)90009-Q.

Boubee, J.A.T., and Ward, F.J., 1997, Mouth gape, food 

size, and diet of the common smelt Retropinna retropinna 

(Richardson) in the Waikato River system, North 

Island, New Zealand: New Zealand Journal of Marine 

and Freshwater Research, v. 31, no. 2, p. 147–154, 

https://doi.org/10.1080/00288330.1997.9516753.

Boyd, S.E., Limpenny, D.S., Rees, H.L., and 

Cooper, K.M., 2005, The effects of marine sand and 

gravel extraction on the macrobenthos at a commercial 

dredging site (results 6 years post-dredging): ICES 

Journal of Marine Science, v. 62, no. 2, p. 145–162, 

https://doi.org/10.1016/j.icesjms.2004.11.014.

Brey, T., 2001, Population dynamics in benthic 

invertebrates—A virtual handbook: Version 01.2, 

http://www.thomas-brey.de/science/virtualhandbook.

Brey, T., Rumohr, H., and Ankar, S., 1988, Energy content 

of macrobenthic invertebrates—General conversion 

factors from weight to energy: Journal of Experimental 

Marine Biology and Ecology, v. 117, no. 3, p. 271–278, 

https://doi.org/10.1016/0022-0981(88)90062-7.

Buechner, H., Matheson, L., and Simenstad, C.A, 1981, Food 

web relationships of juvenile salmonids and English sole, 

section 8.0 in Simenstad, C.A., and Eggers, D.M., eds., 

Juvenile salmonid and baitfish distribution, abundance, 

and prey resources in selected areas of Grays Harbor, 

Washington: University of Washington, Fisheries Research 

Institute, p. 146–185.

Burnham, K.P., and Anderson, D.R., 2002, Model 

selection and multimodel inference—A practical 

information-theoretic approach 2nd ed.: New York, 

Springer-Verlag, 515 p., http://ecologia.ib.usp.br/bie5782/

lib/exe/fetch.php?media=bie5782:pdfs:burnham_

anderson2002.pdf.

California Department of Fish and Wildlife, 2013, San 

Francisco Bay Study—1980–2012 dataset: available 

from http://www.dfg.ca.gov/delta/ProjectDescription.asp?

ProjectID=BAYSTUDY.

California State Coastal Conservancy, California Ocean 

Protection Council, NOAA National Marine Fisheries 

Service and Restoration Center, San Francisco Bay 

Conservation and Development Commission, and San 

Francisco Estuary Partnership, 2010, San Francisco Bay 

subtidal habitat goals report; Conservation planning for 

the submerged areas of the bay; 50-year conservation 

plan: California State Coastal Conservancy, 180 p., 

http://www.sfbaysubtidal.org/PDFS/Full%20Report.pdf.

Cardoso, I., Granadeiro, J.P., and Cabral, H., 2010, Benthic 

macroinvertebrates’ vertical distribution in the Tagus 

estuary (Portugal)—The influence of tidal cycle: Estuarine, 

Coastal and Shelf Science, v. 86, no. 4, p. 580–586, 

https://doi.org/10.1016/j.ecss.2009.11.024.

Cauffope, G., and Heymans, S.J.J., 2005, Energy contents 

and conversion factors for sea lion’s prey, in Guenette, S., 

and Christensen, V., eds., Food web models and data for 

studying fisheries and environmental impacts on Eastern 

Pacific ecosystems—Fisheries Centre Research Reports 

v. 13: Canada, University of British Columbia, p. 225–237.

Chapman, J.W., 1988, Invasions of the northeast Pacific 

by Asian and Atlantic Gammaridean amphipod 

crustaceans, including a new species of Corophium: 

Journal of Crustacean Biology, v. 8, no. 3, p. 364–382, 

https://doi.org/10.1163/193724088X00242.

Chigbu, P., Sibley, T.H., and Beauchamp, D.A., 1998, 

Abundance and distribution of Neomysis mercedis and 

a major predator, longfin smelt (Spirinchus thaleichthys) 

in Lake Washington: Hydrobiologia, v. 386, no. 1–3, 

p. 167–182, https://doi.org/10.1023/A:1003537122340.

Clarke, D.G., 1986, Benthic resources assessment technique 

evaluation of disposal sites in Puget Sound and adjacent 

waters: U.S. Corps of Engineers, Vicksburg, Miss., 72 p., 

https://apps.dtic.mil/dtic/tr/fulltext/u2/a184926.pdf.

Clarke, D.G., Ray, G.L., and Bass, R.J., 1993, Benthic 

recovery on experimental dredged material disposal mounds 

in Galveston Bay, Texas: The Second State of the Bay 

Symposium, February 4–6, 1993, p. 191–197.

Clarke, D.G., Engler, R.M., and Wilber, D.H., 2000, 

Assessment of potential impacts of dredging 

operations due to sediment resuspension: DOER, 

Army Engineer Waterways Experiment Station, 

Vicksburg, Miss., ERDC-TN-DOER-E9, 14 p., 

https://apps.dtic.mil/dtic/tr/fulltext/u2/a377325.pdf.

Cloern, J.E., Cole, B.E., Edmunds, J.L., Schraga, T.S., and 

Arnsberg, A., 2000, Patterns of water-quality variability in 

San Francisco Bay during the first six years of the RMP, 

1993–1998: San Francisco Estuary Institute, RMP no. 41, 

19 p., https://www.sfei.org/sites/default/files/biblio_files/

patterns.pdf.

Cohen, A.N., 2010, Habitat stressor narrative descriptions, 

appendix 2–1 of San Francisco Bay subtidal habitat goals 

report: Oakland, Calif., San Francisco Estuary Institute, 

94 p., http://www.sfbaysubtidal.org/PDFS/Ap2-1%20

Habitat%20Stressors.pdf.
References Cited 77

Cohen, A.N., and Carlton, J.T., 1995, Nonindigenous aquatic 

species in a United States estuary—A case study of the 

biological invasions of the San Francisco Bay and Delta: 

Washington, D.C., U.S. Fish and Wildelife Service, 

http://bioinvasions.org/wp-content/uploads/1995-SFBayInvasion-Report.pdf.

Cohen, A.N., and Carlton, J.T., 1998, Accelerating invasion 

rate in a highly invaded estuary: Science, v. 279, no. 5350, 

p. 555–558, https://doi.org/10.1126/science.279.5350.555.

Conomos, T.J., Smith, R.E., and Gartner, J.W., 1985, 

Environmental setting of San Francisco Bay, in Cloern, J.E., 

and Nichols, F.H., eds., Temporal dynamics of an estuary—

San Francisco Bay: Dordrecht, The Netherlands, Springer, 

p. 1–12, https://doi.org/10.1007/978-94-009-5528-8_1.

Cooper, K.M., Barrio Froján, C.R.S., Defew, E., Curtis, M., 

Fleddum, A., Brooks, L., and Paterson, D.M., 2008, 

Assessment of ecosystem function following marine 

aggregate dredging: Journal of Experimental Marine 

Biology and Ecology, v. 366, no. 1–2, p. 82–91, 

https://doi.org/10.1016/j.jembe.2008.07.011.

Crowder, L.B., and Cooper, W.E., 1982, Habitat structural 

complexity and the interaction between Bluegills 

and their prey: Ecology, v. 63, no. 6, p. 1802–1813, 

https://doi.org/10.2307/1940122.

Cumminns, K.W., and Wuycheck, J.C., 1971, Caloric 

equivalents for investigations in ecological energetics: 

Internationale Vereinigung für Theoretische und 

Angewandte Limnologie: Mitteilungen, v. 18, no. 1, 

p. 1–158, https://doi.org/10.1080/05384680.1971.11903918.

Currie, D.R., and Parry, G.D., 1996, Effects of scallop 

dredging on a soft sediment community—A large-scale 

experimental study: Marine Ecology Progress Series, v. 134, 

p. 131–150, https://doi.org/10.3354/meps134131.

De La Cruz, S.E.W., Woo, I., Hobbs, J., Loveland, A., 

Donald, J., and Takekawa, J.Y., 2016, A review of 

Central San Francisco Bay foraging fish and their benthic 

prey resources: Berkeley, California, U.S. Geological 

Survey Administrative Report to San Francisco Estuary 

Institute, 121 p.

De La Cruz, S.E.W., Woo, I., Flanagan, A., Mittelstaedt, H., 

and Donald, J., 2017, Assessing the impact of periodic 

dredging on macroinvertebrate-prey availability for benthic 

foraging fishes—Final study plan and preliminary pilot 

study results: Report to the San Francisco Estuary Institute 

Regional Monitoring Program, 65 p., https://www.sfei.org/

sites/default/files/biblio_files/USGS%20Benthic%20

Recovery%20Project%20Final%20Report_0.pdf.

Dernie, K.M., Kaiser, M.J., and Warwick, R.M., 

2003, Recovery rates of benthic communities 

following physical disturbance: Journal of 

Animal Ecology, v. 72, no. 6, p. 1043–1056, 

https://doi.org/10.1046/j.1365-2656.2003.00775.x.

Desprez, M., 2000, Physical and biological impact of marine 

aggregate extraction along the French coast of the Eastern 

English Channel—Short- and long-term post-dredging 

restoration: ICES Journal of Marine Science, v. 57, no. 5, 

p. 1428–1438, https://doi.org/10.1006/jmsc.2000.0926.

Di Stefano, J., 2003, How much power is enough? Against the 

development of an arbitrary convention for statistical power 

calculations: Functional Ecology, v. 17, no. 5, p. 707–709, 

https://doi.org/10.1046/j.1365-2435.2003.00782.x.

Dumbauld, B.R., Holden, D.L., and Langness, O.P., 

2008, Do sturgeon limit burrowing shrimp populations 

in Pacific Northwest Estuaries?: Environmental 

Biology of Fishes, v. 83, no. 3, p. 283–296, 

https://doi.org/10.1007/s10641-008-9333-y.

Ebert, D.A., and Ebert, T.B., 2005, Reproduction, diet 

and habitat use of leopard sharks, Triakis semifasciata 

(Girard), in Humboldt Bay, California, USA: Marine 

and Freshwater Research, v. 56, no. 8, p. 1089–1098, 

https://doi.org/10.1071/MF05069.

Elliott, M., and Quintino, V., 2007, The estuarine quality 

paradox, environmental homeostasis and the difficulty 

of detecting anthropogenic stress in naturally stressed 

areas: Marine Pollution Bulletin, v. 54, no. 6, p. 640–645, 

https://doi.org/10.1016/j.marpolbul.2007.02.003.

Emmett, R.L., Hinton, S.A., Stone, S.L., and Monaco, M.E., 

1991, Distribution and abundance of fishes and 

invertebrates in west coast estuaries—Volume II —

Species life history summaries: U.S. Department of 

Commerce, NOAA’s Estuarine Living Marine Resources 

Program, Rockville, Md., ftp://ftp.library.noaa.gov/noaa_

documents.lib/NOS/ORCA/ELMR_report/ELMR_11.pdf.

Emmett, R.L., Brodeur, R.D., Miller, T.W., Pool, S.S., 

Krutzikowsky, G.K., Bentley, P.J., and McCrae, J., 2005, 

Pacific sardine (Sardinops sagax) abundance, distribution, 

and ecological relationships in the Pacific Northwest: Page 

California Cooperative Oceanic Fisheries Investigations 

Report, v. 46, p. 122–143, https://www.calcofi.org/

publications/calcofireports/v46/Vol_46_Emmett_et_al_

Pacific_Sardine.pdf.

Espinoza, P., Bertrand, A., van der Lingen, C.D., Garrido, S., 

and Rojas de Mendiola, B., 2009, Diet of sardine 

(Sardinops sagax) in the northern Humboldt current 

system and comparison with the diets of clupeoids in 

this and other eastern boundary upwelling systems: 

Progress in Oceanography, v. 83, no. 1–4, p. 242–250, 

https://doi.org/10.1016/j.pocean.2009.07.045.
78 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Ferraro, S.P., and Cole, F.A., 2004, Optimal benthic 

macrofaunal sampling protocol for detecting 

differences among four habitats in Willapa Bay, 

Washington, USA: Estuaries, v. 27, no. 6, p. 1014–1025, 

https://doi.org/10.1007/BF02803427.

Ferry-Graham, L.A., 1998, Effects of prey size 

and mobility on prey-capture kinematics in 

leopard sharks Triakis semifasciata: The Journal 

of Experimental Biology, v. 201, p. 2433–2444, 

https://jeb.biologists.org/content/201/16/2433.

Feyrer, F., Herbold, B., Matern, S.A., and Moyle, P.B., 2003, 

Dietary shifts in a stressed fish assemblage—Consequences 

of a bivalve invasion in the San Francisco Estuary: 

Environmental Biology of Fishes, v. 67, no. 3, p. 277–288, 

https://doi.org/10.1023/A:1025839132274.

Gadomski, D.M., and Boehlert, G.W., 1984, Feeding 

ecology of pelagic larvae of English sole Parophrys 

vetulus and butter sole Isopsetta isolepis off the Oregon 

coast: Marine Ecology Progress Series, v. 20, p. 1–12, 

https://doi.org/10.3354/meps020001.

Gessner, J., Van Eenennaam, J.P., and Doroshov, S.I., 

2007, North American green and European Atlantic 

sturgeon—Comparisons of life histories and human 

impacts: Environmental Biology of Fishes, v. 79, no. 3–4, 

p. 397–411, https://doi.org/10.1007/s10641-006-9073-9.

Gillet, D.J., Ranasinghe, J.A., and Stein, E.D., 2014, 

Development of benthic community condition indices—

San Francisco Bay—Phase I Final Report: Richmond, 

Calif., Contract #1038, San Francisco Estuary Institute, 

Contribution # 735, 19 p., https://www.sfei.org/sites/default/

files/biblio_files/735_SCCWRP_Mesohaline_Benthic_

Index_Report_Final.pdf.

Goals Project, 1999, Baylands ecosystem habitat goals—A 

report of habitat recommendations prepared by the San 

Francisco Bay Area Wetlands Ecosystem Goals Project: 

Oakland, Calif., U.S. Environmental Protection Agency, San 

Francisco, Calif./San Francisco Bay Regional Water Quality 

Control, https://sfestuary.org/wp-content/uploads/2012/12/

1Habitat_Goals.pdf.

Godin, J.-G.J., and Keenleyside, M.H.A., 1984, Foraging 

on patchily distributed prey by a cichlid fish (Teleostei, 

Cichlidae)—A test of the ideal free distribution 

theory: Animal Behaviour, v. 32, no. 1, p. 120–131, 

https://doi.org/10.1016/S0003-3472(84)80330-9.

Goss-Custard, J.D., West, A.D., Yates, M.G., 

Caldow, R.W., Stillman, R.A., Bardsley, L., Castilla, J., 

Castro, M., Dierschke, V., Durell, S.E., Eichhorn, G., 

Ens, B.J., Exo, K.M., Udayangani-Fernando, P.U., 

Ferns, P.N., Hockey, P.A., Gill, J.A., Johnstone, I., 

Kalejta-Summers, B., Masero, J.A., Moreira, 

F., Nagarajan, R.V., Owens, I.P., Pacheco, C., 

Perez-Hurtado, A., Rogers, D., Scheiffarth, G., Sitters, 

H., Sutherland, W.J., Triplet, P., Worrall, D.H., Zharikov, 

Y., Zwarts, L., and Pettifor, R.A., 2006, Intake rates and 

the functional response in shorebirds (Charadriiformes) 

eating macro-invertebrates: Biological Reviews of the 

Cambridge Philosophical Society, v. 81, no. 4, p. 501–529, 

https://doi.org/10.1111/j.1469-185X.2006.tb00216.x.

Gotshall, D.W., 1977, Stomach contents of northern California 

dungeness crabs, Cancer magister: California Fish and 

Game, v. 63, no. 1, p. 43–51.

Greene, H.G., Endris, C., Vallier, T., Golden, N., Cross, J., 

Ryan, H., Dieter, B., and Niven, E., 2013, Sub-tidal benthic 

habitats of central San Francisco Bay and offshore Golden 

Gate area—A review: Marine Geology, v. 345, p. 31–46, 

https://doi.org/10.1016/j.margeo.2013.05.001.

Greenstein, D.J., and Tiefenthaler, L.L., 2013, Reproduction 

and population dynamics of Grandidierella japonica 

(Stephensen) (Crustacea—Amphipoda) in upper Newport 

Bay: Bulletin of the Southern California Academy of 

Sciences, v. 96, no. 1, p. 34–42.

Grilo, T.F., Cardoso, P.G., Dolbeth, M., Bordalo, 

M.D., and Pardal, M.A., 2011, Effects of extreme 

climate events on the macrobenthic communities’ 

structure and functioning of a temperate estuary: 

Marine Pollution Bulletin, v. 62, no. 2, p. 303–311, 

https://doi.org/10.1016/j.marpolbul.2010.10.010.

Günther, C.-P., 1992, Dispersal of intertidal invertebrates—A 

strategy to react to disturbances of different scales?: 

Netherlands Journal of Sea Research, v. 30, p. 45–56, 

https://doi.org/10.1016/0077-7579(92)90044-F.

Haaker, P.L., 1975, The biology of the California halibut, 

Paralichthys californicus (Ayres), in Anaheim Bay, 

California, in Lane, E.D., and Hill, C.W., eds., The marine 

resources of Anaheim Bay: California Department of Fish 

and Game Fish Bulletin, v. 165, p. 137–159.

Haderlie, E.C., and Abbott, D.P., 1980, Bivalvia—The clams 

and allies, in Morris, R.H., Abbott, D.P., and Haderlie, E.C., 

eds., Intertidal invertebrates of California (1st ed.): 

Stanford, Calif., Stanford University Press, p. 335–411.
References Cited 79

Hanson, C.H., Coil, J., Keller, B., Johnson, J., Taplin, J., and 

Monroe, J., 2004, Assessment and evaluation of the effects 

of sand mining on aquatic habitat and fishery populations of 

central San Francisco Bay and the Sacramento–San Joaquin 

Estuary: Hanson Environmental, Inc.

Hart, J.L., 1973, Pacific fishes of Canada—Ottowa: Fisheries 

Research Board of Canada Bulletin, v. 180, p. 1–740.

Haugen, C.W., 1990, The biological environment of the 

California halibut, Paralichthys californicus: Fish Bulletin, 

v. 174, 475 p.

Herbold, B., 1987, Patterns of co-occurrence and resources use 

in a non-coevolved assemblage of fishes: Ph.D. dissertation, 

University of California, Davis, 68 p.

Hirsch, N.D., DiSalvo, L.H., and Peddicord, R., 

1978, Effects of dredging and disposal on aquatic 

organisms: U.S. Army Corps of Engineers, 

Technical Report DS-78-5, Vicksburg, Miss., 41 p., 

https://apps.dtic.mil/dtic/tr/fulltext/u2/a058989.pdf.

Hobbs, J.A., Bennett, W.A., and Burton, J.E., 2006, Assessing 

nursery habitat quality for native smelts (Osmeridae) 

in the low-salinity zone of the San Francisco estuary: 

Journal of Fish Biology, v. 69, no. 3, p. 907–922, accessed 

April 1, 2014, at http://doi.wiley.com/10.1111/j.1095-

8649.2006.01176.x.

Hogue, E.W., and Carey, A.G., Jr., 1982, Feeding ecology of 

0-age flatfishes at a nursery ground on the Oregon coast: 

Fish Bulletin, v. 80, p. 555–565, accessed February 13, 

2015, at https://agris.fao.org/agris-search/search.do?

recordID=US19840065107.

Holland, A.F., Mountford, N.K., Hiegel, M.H., 

Kaumeyer, K.R., and Mihursky, J.A., 1980, Influence of 

predation on infaunal abundance in Upper Chesapeake 

Bay, USA: Marine Biology, v. 57, no. 3, p. 221–235, 

https://doi.org/10.1007/BF00390739.

Hunter, J., 1977, Behavior and survival of northern anchovy 

Engraulis mordax larvae: Califorina Cooperative 

Oceanic Fisheries Investigations, v. 19, p. 138–146, 

http://calcofi.org/publications/calcofireports/v19/Vol_19_

Hunter.pdf.

Israel, J.A., and Klimley, A.P., 2008, Life history 

conceptual model for North American green sturgeon 

(Acipenser medirostris): Davis, University of California, 

49 p., https://nrm.dfg.ca.gov/FileHandler.ashx?

DocumentID=29310.

Jensen, G.C., and Asplen, M.K., 1998, Omnivory 

in the diet of juvenile dungeness crab, Cancer 

magister Dana: Journal of Experimental Marine 

Biology and Ecology, v. 226, no. 2, p. 175–182, 

https://doi.org/10.1016/S0022-0981(97)00244-X.

Jones, M.L., 1961, Lightiella serendipita gen. nov., 

sp. nov., a cephalocarid from San Francisco Bay, 

California: Crustaceana, v. 3, no. 1, p. 31–46, 

https://doi.org/10.1163/156854061X00518.

Kao, J.S., 2000, Diet, daily ration and gastric evacuation of 

the leopard shark (Triakis semifasciata): A university thesis 

presented to the faculty of California State University, 

Hayward, 96 p.

Kenny, A.J., and Rees, H.L., 1994, The effects of marine 

gravel extraction on the macrobenthos—Early post-dredging 

recolonization: Marine Pollution Bulletin, v. 28, no. 7, p. 

442–447, https://doi.org/10.1016/0025-326X(94)90130-9.

Krone, R.B., 1979, Sedimentation in the San Francisco 

Bay system, in Conomos, T.J., ed., San Francisco Bay—

The urbanized estuary:Pacific Division of the American 

Association for the Advancement of Science, p. 85–96, 

http://downloads.ice.ucdavis.edu/sfestuary/conomos_1979/

archive1020.PDF.

LaSalle, M.W., 1990, Physical and chemical alterations 

associated with dredging—An overview: Seattle, 

Wash., Effects of dredging on anadromous Pacific Coast 

fishes, Workshop Proceedings, p. 1–12.

Lassuy, D.R., 1989, Species profiles—Life histories 

and environmental requirements of coastal fishes and 

invertebrates (Pacific Northwest)—English Sole: 

U.S. Army Corps of Engineers, Biological Report 82, TR 

EL-82-4, 17 p.

Lebednik, P., 2004, Framework for assessment of potential 

effects of dredging on sensitive fish species in San 

Francisco Bay—Final report: Ecosystem Services Group, 

San Francisco, Calif., 141 p.

Lee, H., II, Thompson, B., and Lowe, S., 2003, Estuarine 

and scalar patterns of invasion in the soft-bottom 

benthic communities of the San Francisco estuary: 

Biological Invasions, v. 5, no. 1–2, p. 85–102, 

https://doi.org/10.1023/A:1024038522256.

Leong, R.J.H., and O’Connell, C.P., 1969, A laboratory 

study of particulate and filter feeding of the Northern 

Anchovy (Engraulis mordax): Journal of the Fisheries 

Research Board of Canada, v. 26, no. 3, p. 557–582, 

https://doi.org/10.1139/f69-053.

Longhurst, A.R., 1971, The Clupeoid resources of tropical 

seas: Oceanography and Marine Biology—an Annual 

Review, v. 9, p. 349–385, https://swfsc.noaa.gov/

publications/cr/1971/7128.pdf.

Love, M.S., Yoklavich, M., and Thorsteinson, L., 2002, 

The rockfishes of the northeast Pacific: Berkeley, Calif., 

University of California Press, 416 p.
80 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Lovvorn, J.R., De La Cruz, S.E.W., Takekawa, J.Y., 

Shaskey, L.E., and Richman, S.E., 2013, Niche overlap, 

threshold food densities, and limits to prey depletion 

for a diving duck assemblage in an estuarine bay: 

Marine Ecology Progress Series, v. 476, p. 251–268, 

https://doi.org/10.3354/meps10104.

Lundquist, C.J., Thrush, S.F., Oldman, J.W., and 

Senior, A.K., 2004, Limited transport and recolonization 

potential in shallow tidal estuaries: Limnology 

and Oceanography, v. 49, no. 2, p. 386–395, 

https://doi.org/10.4319/lo.2004.49.2.0386.

Lunz, J.D., and Kendall, D.R., 1982, Benthic resources 

assessment technique, a method for quantifying 

the effects of benthic community changes on 

fish resources: Oceans, v. 82, p. 1021–1027, 

https://doi.org/10.1109/OCEANS.1982.1151822.

Madon, S.P., 2002, Ecophysiology of juvenile California 

halibut Paralichthys californicus in relation to 

body size, water temperature and salinity: Marine 

Ecology Progress Series, v. 243, p. 235–249, 

https://doi.org/10.3354/meps243235.

Markmann, C., 1986, Benthic monitoring in the Sacramento–

San Joaquin Delta—Results from 1975 through 1981: 

Department of Water Resources, Interagency Ecology Study 

Program for the Sacramento-San Joaquin Estuary, Technical 

Report 12, 62 p.

McCabe, G.T., Jr., Emmett, R.L., and Hinton, S.A., 

1993, Feeding ecology of juvenile white sturgeon 

(Acipenser transmontanus) in the lower Columbia 

River: Northwest Science, v. 67, no. 3, p. 170–180, 

http://hdl.handle.net/2376/1588.

McCall, J.N., 1992, Source of harpacticoid copepods in the 

diet of juvenile starry flounder: Marine Ecology Progress 

Series, v. 86, p. 41–50, https://doi.org/10.3354/meps086041.

McCall, P.L., 1977, Community patterns and adaptive 

strategies of infaunal benthos of Long Island Sound: 

Journal of Marine Research, v. 35, no. 2, p. 221–266, 

https://images.peabody.yale.edu/publications/jmr/jmr35-

02-01.pdf.

McFarlane, G., Schweigert, J., Detering, J., and Hodes, V., 

2010, Diet analysis of pacific sardine (Sardinops sagax) 

off the west coast of Vancouver Island, British Columbia 

from 1997 to 2008: California Cooperative Oceanic 

Fisheries Investigations Report, v. 51, p. 169–181, 

https://calcofi.org/publications/calcofireports/v51/Vol51_

CalCOFI_Reports.pdf.

McKechnie, R.J., and Fenner, R.B., 1971, Food habits of 

white sturgeon, Acipenser transmontanus, in San Pablo and 

Suisun bays, California: California Fish and Game, v. 57, 

no. 3, p. 209–212.

Miller, B.S., 1967, Stomach contents of adult starry flounder 

and sand sole in East Sound, Orcas Island, Washington: 

Journal of the Fisheries Research Board of Canada, v. 24, 

no. 12, p. 2515–2526, https://doi.org/10.1139/f67-201.

Miller, M.J., 2004, The ecology and functional morphology 

of feeding of North American Sturgeon and Paddlefish, in

LeBreton, G.T.O., Beamish, W.H., and McKinley, R.S., 

eds., Sturgeons and paddlefish of North America: 

Springer, Dordrecht, The Netherlands, p. 87–102, 

https://doi.org/10.1007/1-4020-2833-4_5.

Miller, T.W., and Brodeur, R.D., 2007, Diets of and trophic 

relationships among dominant marine nekton within the 

northern California current ecosystem: Fish Bulletin, v. 105, 

no. 4, p. 548–559, https://spo.nmfs.noaa.gov/sites/default/

files/pdf-content/2007/1054/miller.pdf.

Moore, J.W., and Moore, I.A., 1976, The basis of food 

selection in flounders, Platichthys flesus (L.), in the Severn 

Estuary: Journal of Fish Biology, v. 9, no. 2, p. 139–156, 

https://doi.org/10.1111/j.1095-8649.1976.tb04669.x.

Motta, P.J., and Wilga, C.D., 2001, Advances in the study 

of feeding behaviors, mechanisms, and mechanics of 

sharks: Environmental Biology of Fishes, v. 60, no. 1–3, 

p. 131–156, https://doi.org/10.1023/A:1007649900712.

Moyle, P.B., 2002, Inland fishes of California, revised and 

expanded: Berkeley, University of California Press, 517 p.

Moyle, P.B., and Davis, L.H., 2000, A list of 

freshwater, anadromous, and euryhaline fishes of 

California: California Fish and Game, v. 86, no. 4, 

p. 244–258, https://nrm.dfg.ca.gov/FileHandler.ashx?

DocumentID=83921.

Muir, W.D., Emmett, R.L., and McConnell, R.J., 1988, Diet of 

juvenile and subadult white sturgeon in the lower Columbia 

River and its estuary: California Fish and Game, v. 74, 

p. 49–54.

Munuera Fernandez, I.M., and Gonzalez-Quiros, R., 

2006, Analysis of feeding of Sebastes auriculatus 

(Walbaum, 1792) larval stages in the central Cantabrian 

Sea: Scientia Marina, v. 70, no. S1, p. 131–139, 

https://doi.org/10.3989/scimar.2006.70s1131.

Newell, R.C., Seiderer, L.J., and Hitchcock, D.R., 1998, 

The impact of dredging works in coastal waters—A 

review of the sensitivity to disturbance and subsequent 

recovery of biological resources on the sea bed: 

Oceanography and Marine Biology, v. 36, p. 127–178, 

https://www.researchgate.net/publication/298415859_

The_impact_of_dredging_works_in_coastal_waters_a_

review_of_the_sensitivity_to_disturbance_and_subsequent_

recovery_of_biological_resources_on_the_sea_bed.
References Cited 81

Nichols, F.H., Cloern, J.E., Luoma, S.N., and 

Peterson, D.H., 1986, The modification of an 

estuary: Science, v. 231, no. 4738, p. 567–573, 

https://doi.org/10.1126/science.231.4738.567.

Nichols, F.H., and Pamatmat, M.M., 1988, The ecology of the 

soft-bottom benthos of San Francisco Bay—A community 

profile: U.S. Fish and Wildlife Service Biological Report 85, 

73 p., https://apps.dtic.mil/dtic/tr/fulltext/u2/a322690.pdf.

Nightingale, B., and Simenstad, C.A., 2001, Executive 

Summary—Overwater structures—Marine 

issues:Washington State Transportation Center (TRAC), 

University of Washington, 6 p., https://www.wsdot.wa.gov/

research/reports/fullreports/508.2.pdf.

Oliver, J.S., Slattery, P.N., Hulberg, L.W., and Nybakken, J.W., 

1977, Patterns of succession in benthic infaunal 

communities following dredging and dredged material 

disposal in Monterey Bay: U.S. Army Engineer Waterways 

Experiment Station, Technical Report D-77-27, 186 p., 

http://aquaticcommons.org/2612/1/Tech_Report_D77-27.pdf.

Orcutt, H.G., 1950, The life history of the starry flounder 

Platichthys stellatus (Pallas): California Department 

of Fish and Game, Fish Bulletin no. 78, 101 p., 

https://escholarship.org/uc/item/3c74b3bj.

Parrish, R.H., Mallicoate, D.L., and Mais, K.F., 

1985, Regional variations in the growth and 

age composition of northern anchovy, Engraulis 

mordax: NOAA National Marine Fisheries 

Service Fishery Bulletin, v. 83, no. 4, p. 483–496, 

https://swfsc.noaa.gov/publications/cr/1985/8567.pdf.

Peterson, H.A., and Vayssieres, M., 2010, Benthic 

assemblage variability in the upper San Francisco 

Estuary—A 27-year retrospective: San Francisco 

Estuary and Watershed Science, v. 8, no. 1, 27 p., 

https://doi.org/10.15447/sfews.2010v8iss1art2.

Piet, G.J., Pfisterer, A.B., and Rijnsdorp, A.D., 

1998, On factors structuring the flatfish 

assemblage in the southern North Sea: Journal 

of Sea Research, v. 40, no. 1–2, p. 143–152, 

https://doi.org/10.1016/S1385-1101(98)00008-2.

Plummer, K.M., Demartini, E.E., and Roberts, D.A., 1983, 

The feeding habits and distribution of juvenile-small 

adult California halibut (Paralichthys californicus) in 

coastal waters off northern San Diego County: California 

Cooperative Oceanic Fisheries Investigations Report, v. 24, 

p. 194–201, http://calcofi.org/publications/calcofireports/

v24/Vol_24_Plummer_etal.pdf.

Quinn, G.P., and Keough, M.J., 2002, Experimental 

design and data analysis for biologists: Cambridge, 

U.K., Cambridge University Press, 558 p., 

https://doi.org/10.1017/CBO9780511806384.

R Development Core Team, 2017, R—A language 

and environment for statistical computing: Vienna, 

Austria, R Foundation for Statistical Computing, 

https://www.R-project.org/.

Radtke, L.D., 1966, Distribution of smelt, juvenile sturgeon, 

and starry flounder in the Sacramento–San Joaquin Delta 

with observations on food of sturgeon: Ecological Studies 

of the Sacramento-San Joaquin Estuary, Part II: Department 

of Fish and Game, Fish Bulletin no. 136, p. 115–119.

Ray, G.L., 2005, Ecological functions of shallow, 

unvegetated estuarine habitats and potential dredging 

impacts (with emphasis on Chesapeake Bay)—

Wetlands Regulatory Assistance Program, Technical 

Notes Collection, ERDC TN-WRAP-05-3: U.S. Army 

Engineer Research and Development Center, Vicksburg, 

Miss., 13 p., https://pdfs.semanticscholar.org/3183/

584e17b7724e69a6bd5db9656feac16c3746.pdf.

Ray, G.L., Clarke, D.G., Engler, R.M., Wilber, D., and 

Brostoff, W., 2005, Sedimentation—Potential biological 

effects of dredging operations in estuarine and marine 

environments: Vicksburg, Miss., U.S. Army Engineer 

Research and Development Center, Technical Note 

DOER-E20, 14 p., https://clu-in.org/download/

contaminantfocus/sediments/potential-biological-effectsdoere20.pdf.

Reecht, Y., Rochet, M.J., Trenkel, V.M., Jennings, S., and 

Pinnegar, J.K., 2013, Use of morphological characteristics 

to define functional groups of predatory fishes in the Celtic 

sea: Journal of Fish Biology, v. 83, no. 2, p. 355–377, 

https://doi.org/10.1111/jfb.12177.

Rees, H.L., and Dare, P.J., 1993, Sources of mortality 

and associated life-cycle traits of selected benthic 

species—A review: Ministry of Agriculture, Fisheries, 

and Food, Fisheries Research Data Report no. 33, 36 p., 

https://www.cefas.co.uk/publications/files/datarep33.pdf.

Reilly, F.J., Clarke, J.U., McFarland, V.A., Lutz, C.H., and 

Jarvis, A.S., 1992, Review and analysis of the literature 

regarding potential impacts of dredged material disposal 

in central San Francisco Bay on fisheries and contaminant 

bioavailability: Vicksburg, Miss., U.S. Army Corps of 

Engineers Waterway Experiment Station, Miscellaneous 

Paper EL-92, 99 p.

Rhoads, D.C., and Germano, J.D., 1986, Interpreting 

long-term changes in benthic community structure—A 

new protocol: Hydrobiologia, v. 142, no. 1, p. 291–308, 

https://doi.org/10.1007/BF00026766.
82 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Ricciardi, A., and Bourget, E., 1998, Weight-to-weight 

conversion factors for marine benthic macroinvertebrates: 

Marine Ecology Progress Series, v. 163, p. 245–251, 

https://doi.org/10.3354/meps163245.

Rich, A.A., 2010, Potential impacts of re-suspended 

sediments associated with dredging and dredged material 

placement on fishes in San Francisco Bay, California—

Literature review and identification of data gaps: 

U.S. Army Corps of Engineers, San Francisco, Calif., 

75 p., https://www.spn.usace.army.mil/Portals/68/docs/

Dredging/LMTS/S%20and%20S/7%20-%20LTMS%20

Literature%20Review__Effects%20of%20Resuspended%20

Sediments.pdf.

Richman, S.E., and Lovvorn, J.R., 2004, Relative foraging 

value to lesser scaup ducks of native and exotic clams from 

San Francisco Bay: Ecological Applications, v. 14, no. 4, 

p. 1217–1231, https://doi.org/10.1890/03-5032.

Roberts, D.E., Smith, A., Ajani, P., and Davis, A.R., 1998a, 

Rapid changes in encrusting marine assemblages exposed 

to anthropogenic point-source pollution—A “Beyond 

BACI” approach: Marine Ecology Progress Series, v. 163, 

p. 213–224, https://doi.org/10.3354/meps163213.

Roberts, R.D., Gregory, M.R., and Foster, B.A., 1998b, 

Developing an efficient macrofauna monitoring index 

from an impact study—A dredge spoil example: 

Marine Pollution Bulletin, v. 36, no. 3, p. 231–235, 

https://doi.org/10.1016/S0025-326X(97)00183-5.

Robinson, H.J., Cailliet, G.M., and Ebert, D.A., 2007, Food 

habits of the longnose skate, Raja rhina (Jordan and 

Gilbert, 1880), in central California waters: Environmental 

Biology of Fishes, v. 80, no. 2–3, p. 165–179, 

https://doi.org/10.1007/s10641-007-9222-9.

Rodil, I.F., Lohrer, A.M., Hewitt, J.E., Townsend, M., 

Thrush, S.F., and Carbines, M., 2013, Tracking 

environmental stress gradients using three biotic integrity 

indices—Advantages of a locally-developed traits-based 

approach: Ecological Indicators, v. 34, p. 560–570, 

https://doi.org/10.1016/j.ecolind.2013.06.023.

Russo, R.A., 1975, Observations on the food habits of leopard 

sharks (Triakis semifasciata) and brown smoothhounds 

(Mustelus henlei): California Fish and Game, v. 61, no. 2, 

p. 95–103.

Schemel, L.E., Ota, A.Y., Harmon, J.G., Shay, J.M., 

and Adorador, R.N., 1988, Benthic macrofauna and 

ancillary data for San Francisco Bay, California, March 

to November 1987: U.S. Geological Survey Open-File 

Report 88–192, 73 p., https://doi.org/10.3133/ofr88192.

Schemel, L.E., Ota, A.Y., Harmon, J.G., Shay, J.M., and 

Adorador, R.M., 1990, Benthic macrofauna and ancillary 

data for San Francisco Bay, California, January to 

November 1988: U.S. Geological Survey Open-File 

Report 89–596, 65 p., https://doi.org/10.3133/ofr89596.

Shellenbarger, G.G., Wright, S.A., and Schoellhamer, D.H., 

2013, A sediment budget for the southern reach in 

San Francisco Bay, CA—Implications for habitat 

restoration: Marine Geology, v. 345, p. 281–293, 

https://doi.org/10.1016/j.margeo.2013.05.007.

Simenstad, C.A., Tanner, C.D., Thom, R.M., and 

Conquest, L.L., 1991, Estuarine habitat assessment 

protocol: Seattle, Wash., National Service Center for 

Environmental Publicaitons, EPA 910/9-91-037, 144 p., 

https://nepis.epa.gov/Exe/ZyPURL.cgi?Dockey=

91024WTI.TXT.

Skinner, J.E., 1962, Sturgeon fishery and status California, 

1962, in Skinner, J.E., ed. Fish and Wildlife Resources 

of the San Francisco Bay Area: California Water 

Projects Branch Report, no. 1, 11 p., Sacramento, Calif., 

http://www.swrcb.ca.gov/waterrights/water_issues/

programs/bay_delta/deltaflow/docs/exhibits/swrcb/swrcb_

skinner1962.pdf.

Stasinopoulos, D.M., and Rigby, R.A., 2007, Generalized 

additive models for location scale and shape (GAMLSS) 

in R: Journal of Statistical Software, v. 23, no. 7, 46 p., 

https://doi.org/10.18637/jss.v023.i07.

Steidl, R.J., Hayes, J.P., and Schauber, E., 1997, Statistical 

power analysis in wildlife research: The Journal 

of Wildlife Management, v. 61, no. 2, p. 270–279, 

https://doi.org/10.2307/3802582.

Stewart, R.A., Luoma, S.N., Schlekat, C.E., Doblin, M.A., 

and Hieb, K.A., 2004, Food web pathway determines how 

selenium affects aquatic ecosystems—A San Francisco Bay 

case study: Environmental Science and Technology, v. 38, 

no. 17, p. 4519–4526, https://doi.org/10.1021/es0499647.

Swain, D., Langenbrunner, B., Neelin, J.D., and Hall, A., 2018, 

Increasing precipitation volatility in twenty-first-century 

California: Nature Climate Change, v. 8, no. 5, p. 427–433, 

https://doi.org/10.1038/s41558-018-0140-y.

Talent, L.G., 1976, Food habits of leopard shark, Triakis 

semifasciata, in Elkhorn Slough, Monterey Bay, California: 

California Fish and Game, v. 62, no. 4, p. 286–298, 

https://www.cabi.org/isc/abstract/19771453560.

Thompson, B., Lowe, S., and Kellogg, M., 2000, Results of 

the benthic pilot study 1994–1997—Part 1—Macrobenthic 

assemblages of the San Francisco Bay-Delta, and their 

responses to abiotic factors: , San Francisco, Calif., San 

Francisco Estuary Institute and the Aquatic Science Center.
References Cited 83

Thompson, B., Ranasinghe, J.A., Lowe, S., Melwani, A., and 

Weisberg, S.B., 2013, Benthic macrofaunal assemblages of 

the San Francisco Estuary and Delta, USA: Environmental 

Monitoring and Assessment, v. 185, no. 3, p. 2281–2295, 

https://doi.org/10.1007/s10661-012-2708-8.

Thompson, J., Hieb, K., McGourty, K., 

Cosentino-Manning, N., Wainwright-De La Cruz, S., 

Elliot, M., and Allen, S., 2007, Habitat type and associated 

biological assemblages—Soft bottom substrate, in 

Schaeffer, K., McGourty, K.R., Cosentio-Manning, N., 

and Allen, S.G., eds., Report on the subtidal habitats and 

associated biological taxa in San Francisco Bay: National 

Oceanic and Atmospheric Administration, p. 37–46.

Toole, C.L., 1980, Intertidal recruitment and feeding in 

relation to optimal utilization of nursery areas by juvenile 

English sole (Parophrys vetulus—Pleuronectidae): 

Environmental Biology of Fishes, v. 5, no. 4, p. 383–390, 

https://doi.org/10.1007/BF00005192.

U.S. Fish and Wildlife Service, 1980, Habitat 

Evaluation Procedures (HEP) ESM 102: 

Washington D.C., Division of Ecological Services, 

https://www.fws.gov/policy/ESM102.pdf.

Underwood, A.J., 1994, On beyond BACI—Sampling 

designs that might reliably detect environmental 

disturbances: Ecological Applications, v. 4, no. 1, p. 3–15, 

https://doi.org/10.2307/1942110.

van Denderen, P.D., van Kooten, T., and Rijnsdorp, A.D., 

2013, When does fishing lead to more fish? 

Community consequences of bottom trawl fisheries 

in demersal food webs: Proceedings of the Royal 

Society B, Biological Sciences, v. 280, no. 1769, 8 p., 

https://doi.org/10.1098/rspb.2013.1883.

Van Der Veer, H.W., Bergman, M.J.N., and Beukema, J.J., 

1985, Dredging activities in the Dutch Wadden 

Sea—Effects on macrobenthic infauna: Netherlands 

Journal of Sea Research, v. 19, no. 2, p. 183–190, 

https://doi.org/10.1016/0077-7579(85)90022-5.

van der Wegen, M., Jaffe, B., Foxgrover, A., and Roelvink, D., 

2017, Mudflat morphodynamics and the impact of sea level 

rise in south San Francisco Bay: Estuaries and Coasts, v. 40, 

no. 1, p. 37–49, https://doi.org/10.1007/s12237-016-0129-6.

van Duren, L.A., and Middelburg, J.J., 2001, The benthic 

boundary layer—Transport processes and biogeochemistry: 

Eos (Washington, D.C.), v. 82, no. 52, p. 658–659, 

https://doi.org/10.1029/01EO00381.

Washington, P.M., Gowan, R., and Ito, D.H., 1978, A 

biological report on eight species of rockfish (Sebastes spp.) 

from Puget Sound, Washington: Seattle, Wash., 

National Oceanic Atmospheric Administration, 50 p., 

https://www.afsc.noaa.gov/Publications/ProcRpt/PR1978_

Washington_rockfish.pdf.

Weigelhofer, G., and Waringer, J., 2003, Vertical 

distribution of benthic macroinvertebrates in riffles 

versus deep runs with differing contents of fine 

sediments (Weidlingbach, Austria): International 

Review of Hydrobiology, v. 88, no. 3–4, p. 304–313, 

https://doi.org/10.1002/iroh.200390027.

Weihs, C., Ligges, U., Luebke, K., and Raabe, N., 2005, 

klaR analyzing German business cycles, in Baier 

D., Decker R., and Schmidt-Thieme, L., eds., Data 

analysis and decision support: Berlin, Springer Verlag, 

p. 335–343 , https://doi.org/10.1007/3-540-28397-8_36.

Wilber, D.H., and Clarke, D.G., 2007, Defining and assessing 

benthic recovery following dredging and dredged material 

disposal: Orlando, Fla., World Dredging Congress.

Wilber, D.H., Ray, G.L., Clarke, D.G., and Diaz, R.J., 2008, 

Responses of benthic infauna to large-scale sediment 

disturbance in Corpus Christi Bay, Texas: Journal of 

Experimental Marine Biology and Ecology, v. 365, no. 1, 

p. 13–22, https://doi.org/10.1016/j.jembe.2008.07.029.

Yang, M.S., 2007, Food habits and diet overlap of seven 

skate species in the Aleutian Islands: NOAA Technical 

Memorandum NMFS-AFSC-177, 47 p.
84 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay
 85

Appendix 1.

Supplemental tables and figures

Table 1.1. GLMM results for total density of 0–4 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.107 0.203 10.365 <0.001

Treatment: 

undredged 0.332 0.063 5.284 <0.001

Season: winter 0.490 0.112 4.368 <0.001

Salinity 0.033 0.007 5.062 <0.001

Elevation –0.200 0.055 –3.652 <0.001

Table 1.2. GLMM results for total density of 4–12 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 1.914 0.238 8.048 <0.001

Treatment: 

undredged

0.402 0.072 5.588 <0.001

Season: winter –0.797 0.142 –5.611 <0.001

Salinity –0.033 0.008 –4.111 <0.001

Elevation –0.279 0.058 –4.780 <0.001

Table 1.3. GLMM results for total density of 12–24 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 1.330 0.346 3.842 <0.001

Treatment: 

undredged

0.302 0.090 3.347 0.001

Season: winter –0.783 0.279 –2.801 0.005

Salinity –0.018 0.012 –1.555 0.120

Elevation 0.182 0.078 2.343 0.019

Table 1.4. GLMM results for total density of 24–50 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept –1.252 1.815 –0.690 0.490

Treatment: 

undredged

0.359 0.114 3.149 0.002

Season: winter 1.186 1.693 0.700 0.484

Salinity 0.042 0.064 0.664 0.507

Elevation –0.239 0.217 –1.102 0.271
86 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 1.5. GLMM results for total density of 0–50 mm 

macroinvertebrates from 0 to 10 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.834 0.194 14.586 <0.001

Treatment: 

undredged

0.420 0.061 6.927 <0.001

Season: winter 0.243 0.107 2.268 0.024

Salinity 0.014 0.006 2.279 0.023

Elevation –0.187 0.053 –3.538 <0.001

Table 1.6. GLMM results for total density of 0–50 mm 

macroinvertebrates from 0 to 10 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2015–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 3.531 0.146 24.227 <0.001

Treatment: 

undredged

0.458 0.059 7.730 <0.001

Season: winter –0.161 0.069 –2.326 0.020

Salinity –0.010 0.005 –2.174 0.030

Elevation –0.203 0.053 –3.843 <0.001

Table 1.8. GLMM results for total biomass of 4–12 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.548 0.429 12.936 <0.001

Treatment: 

undredged

0.610 0.151 4.050 <0.001

Season: winter –3.464 0.258 –13.429 <0.001

Salinity –0.074 0.015 –5.046 <0.001

Elevation –0.100 0.123 –0.813 0.417

Table 1.7. GLMM results for total biomass of 0–4 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept –1.233 0.287 –4.294 <0.001

Treatment: 

undredged

0.736 0.100 7.336 <0.001

Season: winter 1.229 0.172 7.147 <0.001

Salinity 0.135 0.010 14.081 <0.001

Elevation 0.241 0.083 2.919 0.004
Appendix 1. 87

Table 1.9. GLMM results for total biomass of 12–24 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 6.704 0.412 16.254 <0.001

Treatment: 

undredged

–0.226 0.108 –2.100 0.036

Season: winter –0.938 0.339 –2.765 0.006

Salinity –0.022 0.014 –1.589 0.112

Elevation 0.294 0.093 3.161 0.002

Table 1.10. GLMM results for total biomass of 24–50 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 24.185 1.828 13.227 <0.001

Treatment: 

undredged

0.159 0.116 1.376 0.169

Season: winter –16.280 1.706 –9.540 <0.001

Salinity –0.625 0.064 –9.722 <0.001

Elevation –1.326 0.221 –6.004 <0.001

Table 1.11. GLMM results for total biomass of 0–50 mm 

macroinvertebrates from 0 to 10 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.658 0.309 18.292 <0.001

Treatment: 

undredged

1.022 0.120 8.537 <0.001

Season: winter –1.943 0.184 –10.554 <0.001

Salinity –0.027 0.011 –2.534 0.012

Elevation –0.296 0.095 –3.110 0.002

Table 1.12. GLMM results for total energy of 0–4 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 1.370 0.289 4.746 <0.001

Treatment: 

undredged

0.710 0.102 6.985 <0.001

Season: winter 1.294 0.174 7.442 <0.001

Salinity 0.142 0.010 14.707 <0.001

Elevation 0.247 0.084 2.929 0.004
88 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 1.13. GLMM results for total energy of 4–12 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.693 0.364 15.656 <0.001

Treatment: 

undredged

0.595 0.123 4.852 <0.001

Season: winter –2.246 0.217 –10.347 <0.001

Salinity –0.039 0.012 –3.096 0.002

Elevation –0.170 0.099 –1.713 0.087

Table 1.14. GLMM results for total energy of 12–24 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 6.867 0.447 15.365 <0.001

Treatment: 

undredged

–0.085 0.117 –0.728 0.467

Season: winter –0.022 0.370 –0.060 0.952

Salinity 0.013 0.015 0.829 0.408

Elevation 0.345 0.101 3.410 0.001

Table 1.16. GLMM results for total energy of 0–50 mm 

macroinvertebrates from 0 to 10 cm depth at six sites with 

dredged and undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.936 0.282 21.056 <0.001

Treatment: 

undredged

1.083 0.107 10.088 <0.001

Season: winter –0.414 0.171 –2.417 0.016

Salinity 0.031 0.010 3.207 0.001

Elevation 0.023 0.086 0.262 0.794

Table 1.15. GLMM results for total energy of 24–50 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor) with dredged and 

undredged areas.

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 23.253 1.793 12.968 <0.001

Treatment: 

undredged

0.131 0.114 1.154 0.249

Season: winter –14.339 1.674 –8.568 <0.001

Salinity –0.551 0.063 –8.736 <0.001

Elevation –1.149 0.216 –5.310 <0.001
Appendix 1. 89

Table 1.17. GLMM results for the effects of distance from a 

dredged area on total density of 0–4 mm macroinvertebrates from 

0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.283 0.202 11.283 <0.001

Distance from 

dredged area

–0.002 0.001 –2.030 0.043

Season: winter 0.496 0.112 4.445 <0.001

Salinity 0.034 0.007 5.260 <0.001

Elevation –0.238 0.054 –4.427 <0.001

Table 1.18. GLMM results for the effects of distance from a 

dredged area on total density of 4–12 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and Yacht 

Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.015 0.238 8.451 <0.001

Distance from 

dredged area

0.004 0.001 4.361 <0.001

Season: winter –0.810 0.143 –5.678 <0.001

Salinity –0.034 0.008 –4.248 <0.001

Elevation –0.347 0.058 –6.005 <0.001

Table 1.19. GLMM results for the effects of distance from a 

dredged area on total density of 12–24 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 1.377 0.341 4.040 <0.001

Distance from 

dredged area

0.003 0.001 2.969 0.003

Season: winter –0.765 0.280 –2.737 0.006

Salinity –0.017 0.012 –1.506 0.133

Elevation 0.093 0.078 1.190 0.235

Table 1.20. GLMM results for the effects of distance from a 

dredged area on total density of 0–50 mm macroinvertebrates 

from 0 to 10 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and Yacht 

Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 3.018 0.194 15.586 <0.001

Distance from 

dredged area

–0.001 0.001 –0.801 0.423

Season: winter 0.253 0.107 2.377 0.018

Salinity 0.016 0.006 2.477 0.013

Elevation –0.233 0.052 –4.468 <0.001
90 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 1.21. GLMM results for the effects of distance from a 

dredged area on total density of 0–50 mm macroinvertebrates 

from 0 to 10 cm depth at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2015–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 3.716 0.146 25.522 <0.001

Distance from 

dredged area

0.001 0.001 0.669 0.504

Season: winter –0.157 0.069 –2.256 0.024

Salinity –0.009 0.005 –2.034 0.042

Elevation –0.249 0.052 –4.765 <0.001

Table 1.22. GLMM results for the effects of distance from a 

dredged area on total biomass of 0–4 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept –0.811 0.282 –2.879 0.004

Distance from 

dredged area

–0.002 0.001 –2.076 0.038

Season: winter 1.196 0.162 7.389 <0.001

Salinity 0.134 0.009 14.476 <0.001

Elevation 0.075 0.081 0.926 0.355

Table 1.24. GLMM results for the effects of distance 

from a dredged area on total biomass taxa of 12–24 mm 

macroinvertebrates from 0 to 4 cm depth at six sites (Loch 

Lomond, Mooring Road, Paradise Cay, Richardson Bay, 

Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 6.622 0.409 16.179 <0.001

Distance from 

dredged area

–0.001 0.001 –0.809 0.419

Season: winter –0.944 0.339 –2.786 0.005

Salinity –0.022 0.014 –1.601 0.110

Elevation 0.333 0.093 3.571 <0.001

Table 1.23. GLMM results for the effects of distance from a 

dredged area on total biomass of 4–12 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.712 0.428 13.353 <0.001

Distance from 

dredged area

0.003 0.002 1.502 0.134

Season: winter –3.441 0.258 –13.321 <0.001

Salinity –0.073 0.015 –4.975 <0.001

Elevation –0.176 0.121 –1.452 0.147
Appendix 1. 91

Table 1.25. GLMM results for the effects of distance from a 

dredged area on total biomass of 24–50 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 24.247 1.857 13.059 <0.001

Distance from 

dredged area

0.001 0.002 0.518 0.605

Season: winter –16.240 1.725 –9.416 <0.001

Salinity –0.624 0.065 –9.563 <0.001

Elevation –1.287 0.220 –5.852 <0.001

Table 1.26. GLMM results for the effects of distance from a 

dredged area on total biomass of 0–50 mm macroinvertebrates 

from 0 to 10 cm depth at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.587 0.307 18.198 <0.001

Distance from 

dredged area

0.008 0.001 5.529 <0.001

Season: winter –1.758 0.173 –10.165 <0.001

Salinity –0.020 0.010 –1.942 0.053

Elevation –0.512 0.094 –5.452 <0.001

Table 1.27. GLMM results for the effects of distance from a 

dredged area on total energy of 0–4 mm macroinvertebrates from 

0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 1.764 0.283 6.242 <0.001

Distance from 

dredged area

–0.003 0.001 –2.154 0.032

Season: winter 1.266 0.164 7.740 <0.001

Salinity 0.142 0.009 15.227 <0.001

Elevation 0.088 0.082 1.068 0.286

Table 1.28. GLMM results for the effects of distance from a 

dredged area on total energy of 4–12 mm macroinvertebrates from 

0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.841 0.363 16.097 <0.001

Distance from 

dredged area

0.003 0.001 1.874 0.061

Season: winter –2.213 0.217 –10.203 <0.001

Salinity –0.037 0.012 –2.962 0.003

Elevation –0.226 0.098 –2.298 0.022
92 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 1.29. GLMM results for the effects of distance from a 

dredged area on total energy of 12–24 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 6.883 0.446 15.438 <0.001

Distance from 

dredged area

–0.002 0.001 –1.088 0.277

Season: winter –0.025 0.371 –0.067 0.946

Salinity 0.013 0.015 0.815 0.415

Elevation 0.391 0.101 3.853 <0.001

Table 1.30. GLMM results for the effects of distance from a 

dredged area on total energy of 24–50 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 23.345 1.821 12.818 <0.001

Distance from 

dredged area

0.001 0.002 0.568 0.570

Season: winter –14.343 1.692 –8.478 <0.001

Salinity –0.552 0.064 –8.615 <0.001

Elevation –1.108 0.215 –5.148 <0.001

Table 1.32. GLMM results for the effects time since an area was 

dredged on total density of 0–4 mm macroinvertebrates from 0 

to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.457 0.329 7.473 <0.001

Years since an area 

was dredged

0.088 0.060 1.463 0.144

Season: winter 0.421 0.195 2.159 0.032

Salinity 0.018 0.011 1.690 0.092

Elevation 0.118 0.080 1.474 0.141

Table 1.31. GLMM results for the effects of distance from a 

dredged area on total energy of 0–50 mm macroinvertebrates 

from 0 to 10 cm depth at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 5.931 0.279 21.223 <0.001

Distance from 

dredged area

0.006 0.001 4.669 <0.001

Season: winter –0.240 0.161 –1.492 0.136

Salinity 0.039 0.009 4.117 <0.001

Elevation –0.223 0.085 –2.624 0.009
 93

Table 1.33. GLMM results for the effects time since an area was 

dredged on total density of 4–12 mm macroinvertebrates from 0 

to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 1.998 0.350 5.706 <0.001

Years since an area 

was dredged

0.160 0.071 2.257 0.025

Season: winter –0.927 0.223 –4.156 <0.001

Salinity –0.050 0.012 –4.023 <0.001

Elevation –0.228 0.081 –2.822 0.005

Table 1.34. GLMM results for the effects time since an area was 

dredged on total density of 12–24 mm macroinvertebrates from 0 

to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 0.492 0.438 1.124 0.262

Years since an area 

was dredged

0.193 0.079 2.451 0.015

Season: winter –0.679 0.320 –2.122 0.035

Salinity –0.002 0.013 –0.167 0.868

Elevation 0.125 0.102 1.229 0.220

Table 1.35. GLMM results for the effects time since an area was 

dredged on total density of 0–50 mm macroinvertebrates from 0 

to 10 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.753 0.315 8.753 <0.001

Years since an area 

was dredged

0.197 0.058 3.383 0.001

Season: winter 0.157 0.188 0.837 0.403

Salinity 0.006 0.011 0.597 0.551

Elevation 0.105 0.077 1.363 0.174

Table 1.36. GLMM results for the effects time since an area was 

dredged on total density of 0–50 mm macroinvertebrates from 0 

to 10 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2015–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 3.636 0.230 15.794 <0.001

Years since an area 

was dredged

0.153 0.059 2.601 0.010

Season: winter –0.245 0.125 –1.965 0.050

Salinity –0.018 0.007 –2.530 0.012

Elevation 0.182 0.076 2.384 0.018

Appendix 1.
94 Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay

Table 1.37. GLMM results for the effects of time since an area 

was dredged on total biomass of 0–4 mm macroinvertebrates from 

0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept –0.711 0.525 –1.354 0.177

Years since an area 

was dredged

1.918 0.093 20.524 <0.001

Season: winter –2.938 0.283 –10.398 <0.001

Salinity –0.035 0.016 –2.159 0.032

Elevation 0.357 0.121 2.945 0.003

Table 1.38. GLMM results for the effects of time since an area 

was dredged on total biomass of 4–12 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 3.525 0.685 5.147 <0.001

Years since an area 

was dredged

1.027 0.140 7.321 <0.001

Season: winter –3.771 0.408 –9.251 <0.001

Salinity –0.101 0.023 –4.441 <0.001

Elevation –0.332 0.175 –1.896 0.059

Table 1.40. GLMM results for the effects of time since an area 

was dredged on total biomass of 0–50 mm macroinvertebrates 

from 0 to 10 cm depth at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.904 0.485 5.985 <0.001

Years since an area 

was dredged

2.178 0.092 23.704 <0.001

Season: winter –4.753 0.283 –16.787 <0.001

Salinity –0.103 0.016 –6.417 <0.001

Elevation 0.099 0.122 0.817 0.414

Table 1.39. GLMM results for the effects of time since an area 

was dredged on total biomass of 12–24 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 8.774 0.588 14.925 <0.001

Years since an area 

was dredged

–0.239 0.106 –2.253 0.025

Season: winter –2.068 0.436 –4.744 <0.001

Salinity –0.071 0.018 –3.982 <0.001

Elevation 0.189 0.136 1.387 0.167
Appendix 1. 95

Table 1.41. GLMM results for the effects of time since an area 

was dredged on total energy of 0–4 mm macroinvertebrates from 

0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 2.163 0.529 4.090 <0.001

Years since an area 

was dredged

1.919 0.095 20.220 <0.001

Season: winter –2.977 0.285 –10.436 <0.001

Salinity –0.039 0.016 –2.361 0.019

Elevation 0.343 0.123 2.794 0.006

Table 1.42. GLMM results for the effects of time since an area 

was dredged on total energy of 4–12 mm macroinvertebrates from 

0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, Paradise 

Cay, Richardson Bay, Strawberry Channel, and Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 4.788 0.561 8.542 <0.001

Years since an area 

was dredged

0.868 0.112 7.737 <0.001

Season: winter –3.054 0.334 –9.135 <0.001

Salinity –0.089 0.019 –4.737 <0.001

Elevation –0.411 0.137 –3.008 0.003

Table 1.43. GLMM results for the effects of time since an area 

was dredged on total energy of 12–24 mm macroinvertebrates 

from 0 to 4 cm depth at six sites (Loch Lomond, Mooring Road, 

Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 9.970 0.523 19.072 <0.001

Years since an area 

was dredged

–0.285 0.094 –3.027 0.003

Season: winter –1.919 0.388 –4.948 <0.001

Salinity –0.067 0.016 –4.220 <0.001

Elevation 0.185 0.122 1.524 0.129

Table 1.44. GLMM results for the effects of time since an area 

was dredged on total energy of 0–50 mm macroinvertebrates 

from 0 to 10 cm depth at six sites (Loch Lomond, Mooring 

Road, Paradise Cay, Richardson Bay, Strawberry Channel, and 

Yacht Harbor).

[Cores were collected during summer and winter 2016–17. Collection 

site and transects were included in the GLMM as random effects. 

Abbreviation: <, less than]

Fixed effect Estimate Standard 

error

t-value p

Intercept 4.857 0.469 10.356 <0.001

Years since an area 

was dredged

1.868 0.085 22.057 <0.001

Season: winter –3.754 0.262 –14.331 <0.001

Salinity –0.077 0.015 –5.102 <0.001

Elevation 0.288 0.115 2.511 0.013
Figure 1.1. Conceptual diagram illustrating the comparison between an undredged benthic habitat (left), a recently a dredged area (center), and 2–4 activity (right). Undredged areas are characterized by an abundant and diverse prey base of benthic infauna of varying size and depths. Turbidity is ststratified with smaller grains dominating the top 10-cm. Recently dredged areas result in the direct removal of shallow benthic habitat, resulting in incsediment. Post-dredging habitat is partially recovered, with medium sediment grain size providing habitat for smaller soft-bodied prey items. (Change panes indicates a conceptual shift in density, size, or magnitude. MHHW = Mean Higher High Water; MSL = Mean Sea Level; MLLW = Mean Lower Lo
For more information concerning the research in this report, contact the

Director, Western Ecological Research Center

U.S. Geological Survey

3020 State University Drive East

Sacramento, California 95819

https://www.usgs.gov/centers/werc

Publishing support provided by the U.S. Geological Survey 

Science Publishing Network, Sacramento Publishing Service Center
De La Cruz and others—Impacts of Periodic Dredging on Macroinvertebrate Prey Availability for Benthic Foraging Fishes in Central San Francisco Bay, 

California—OFR 2020–1086

ISSN 2331-1258 (online)

https://doi.org/10.3133/ofr20201086