The U.S. Geological Survey is 125 years old this year, 2004.

COVER: The cover image is a panoramic photograph of San Francisco Bay looking eastward from the Marin 

Headlands over the Golden Gate Bridge. Caption follows:

Shifting Shoals and Shattered Rocks—

How Man Has Transformed the Floor of 

West-Central San Francisco Bay

With 3-D Map Supplement

Circular 1259

U.S. Department of the Interior

U.S. Geological Survey
Cover—San Francisco Bay is one of the world’s fi nest natural harbors and a major center for maritime trade. Since the 1850’s, the margins and fl oor of the bay have 

been greatly modifi ed by human activity. Several submerged bedrock knobs in the central bay protrude through the sediment of the bay fl oor and rise to within about 

40 feet (12 m) of the water surface. These rocks have been lowered by blasting several times in the past, but they remain a potential hazard to shipping because cargo 

vessels transiting the bay increasingly have deeper drafts. This panoramic view from the Marin Headlands shows a large container vessel passing beneath the Golden 

Gate Bridge and entering west-central San Francisco Bay. The San Francisco-Oakland Bay Bridge, in the distance to the left of the San Francisco skyline, connects 

to Yerba Buena Island, Alcatraz Island (back cover) is just to the left of the northern pylon of the Golden Gate Bridge, and the low-relief feature just above Alcatraz is 

Treasure Island. (USGS Photograph by Michael F. Diggles.) 
Shifting Shoals and Shattered Rocks—How Man Has 

Transformed the Floor of West-Central San Francisco Bay

By John L. Chin, Florence L. Wong, and Paul R. Carlson

Circular 1259

U.S. Department of the Interior

U.S. Geological Survey

With 3-D Map Supplement

Under San Francisco Bay—

A New View of the Floor of West-Central San Francisco Bay

By David A. Cacchione, Paul R. Carlson, Pat F. Chavez, Jr., John L. Chin, 

Peter Dartnell, James V. Gardner, Helen Gibbons, David M. Rubin, 

Miguel Velasco, and Florence L. Wong
ii 

U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2004

Available from U.S. Geological Survey Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

This report and any updates to it are available at http://geopubs.wr.usgs.gov/circular/c1259/

Additional USGS publications can be found at http://geology.usgs.gov/products.html/

For more information about the USGS and its products;

Telephone: 1-888-ASK-USGS (1-888-275-8747)

World Wide Web: http://www.usgs.gov/

Any use of trade, product, or firm names in this publication is for descriptive purposes only and does 

not imply endorsement of the U.S. Government.

Although this report is in the public domain, it contains copyrighted materials that are noted in 

the text. Permission to reproduce those items must be secured from the individual copyright owners. 

Cataloging-in-publication data are on file with the Library of Congress (http://www.loc.gov/)

Text and illustrations edited by Peter H. Stauffer and James W. Hendley II

Design, layout, and production by Susan E. Mayfield

Published in the Western Region, Menlo Park, California

Manuscript approved for publication, July 8, 2003

ISBN 0-607-94342-4
 iii

Contents

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

San Francisco Bay and Its History............................................................................................................. 1

General Description ............................................................................................................................ 1

The Bay Ecosystem ............................................................................................................................. 1

Human Influence on San Francisco Bay ......................................................................................... 5

Central Bay’s Bedrock Knobs ............................................................................................................ 7

Studies of the Bay......................................................................................................................................... 8

Previous Work ...................................................................................................................................... 8

Recent USGS Studies of West-Central San Francisco Bay.......................................................... 8

Areas and Issues of West-Central San Francisco Bay .......................................................................... 9

Point Knox Shoal.................................................................................................................................. 9

Origin of the Topographic Depression on Point Knox Shoal.............................................. 11

The Disrupted Zone on Point Knox Shoal ............................................................................. 13

Presidio Shoal .................................................................................................................................... 14

Bedrock Knobs................................................................................................................................... 18

Alcatraz Disposal Site....................................................................................................................... 23

Dredging Issues ................................................................................................................................. 23

Sand Mining in West-Central Bay.......................................................................................... 23

Maintenance and Improvement Dredging ........................................................................... 25

Conclusion ................................................................................................................................................... 28

Acknowledgments...................................................................................................................................... 28

References................................................................................................................................................... 28
iv 

Figures

1. Map of San Francisco Bay region as it was in the mid-1850’s.................................................... 2

2. Bathymetric map and shaded-relief image of west-central San Francisco Bay..................... 3

3. Map showing historical changes to the bay margins in the City of San Francisco ................ 4

4. Photograph of mining with high-pressure water cannons in the Gold Rush............................ 5

5. Bathymetric map of bedrock knobs in San Francisco Bay.......................................................... 6

6. Sketch of Arch Rock before modification, showing the opening visible at low tide............... 7

7. Photograph of the blasting of Arch Rock in 1901 .......................................................................... 7

8. Diagram of the multibeam sidescan-sonar mapping technique................................................. 8

9. Map showing the bottom types in west-central San Francisco Bay......................................... 9

10. Map showing lease areas for borrow pits on Point Knox Shoal in the 1930’s.......................... 10

11. Aerial photograph of Treasure Island at the time of the Golden Gate International 

Exposition............................................................................................................................................. 11

12. Bathymetric profile and map of the borrow area near Alameda................................................ 12

13. Sidescan-sonar imagery of the bay floor in the disturbed zone on Point Knox Shoal............ 13

14. Map of lease areas for sand extraction in west-central San Francisco Bay........................... 15

15. Sidescan-sonar imagery of recent dredge-related features on Point Knox Shoal ................. 16

16. Sidescan-sonar imagery of elongate and circular to semicircular depressions on the 

periphery of the Point Knox Shoal disrupted zone........................................................................ 17

17. Sidescan-sonar imagery of dredge-related features on Presidio Shoal .................................. 18

18. Sidescan-sonar imagery of the top of Shag Rock......................................................................... 19

19. Diagram showing the increasing draft of cargo vessels with time............................................ 20

20. Map showing ship lanes for deep-draft vessels in west-central San Francisco Bay ............ 21

21. Photograph of a large container vessel unloading at the Port of Oakland............................... 22

22. Combination photograph/diagram showing a large oil tanker above and below waterline.. 22

23. Perspective views and cross section showing the evolution of the Alcatraz Disposal Site 

through time......................................................................................................................................... 24

24. Maps showing the original extent of wetlands in the Bay-Delta region and what has 

happened to them............................................................................................................................... 26

Map Supplement and 3-D glasses

[In pocket]

Under San Francisco Bay—A new view of the floor of west-central San Francisco Bay
 v
vi 

A large container ship traveling in the eastbound vessel-traffic lane in the vicinity of submerged Blossom Rock as 

it begins to pass between Treasure Island and downtown San Francisco on its way to the Port of Oakland. (USGS 

Photograph by Michael F. Diggles.)
Introduction

San Francisco Bay, one of the world’s finest natural harbors and a major center for maritime trade, is referred to as the 

“Gateway to the Pacific Rim.” The bay is an urbanized estuary 

that is considered by many to be the major estuary in the United 

States most modified by man’s activities (Nichols and others, 

1986). The population around the estuary has grown rapidly 

since the 1850’s and now exceeds 7 million people. The San 

Francisco Bay area’s economy ranks as one of the largest in the 

world, larger even than that of many countries. More than 10 

million tourists are estimated to visit the bay region each year 

(San Francisco Convention and Visitors Bureau, unpub. data 

accessed online August 21, 2002 at http://www.sfvisitor.org). 

The bay area’s population and associated development have 

increasingly changed the estuary and its environment.

San Francisco Bay and the contiguous Sacramento-San 

Joaquin Delta encompass roughly 1,600 square miles (4,100 km2) 

and are the outlet of a major watershed that drains more than 40 

percent of the land area of the State of California (fig. 1). This 

watershed provides drinking water for 20 million people (twothirds of the State’s population) and irrigates 4.5 million acres of 

farmland and ranchland (Friends of the Estuary, 1997).

During the past several decades, much has been done to 

clean up the environment and waters of San Francisco Bay. Conservationist groups have even bought many areas on the margins 

of the bay with the intention of restoring them to a condition 

more like the natural marshes they once were. However, many of 

the major manmade changes to the bay’s environment occurred 

so long ago that the nature of them has been forgotten (Nichols 

and others, 1986). In addition, many changes continue to occur 

today, such as the introduction of exotic species and the loss of 

commercial and sport fisheries because of declining fish populations. The economy and population of the nine counties that 

surround the bay continue to grow and put increasing pressure 

on the bay, both direct and indirect. Therefore, there are mixed 

signals for the future health and welfare of San Francisco Bay.

The San Francisco Bay estuary consists of three subembayments—north bay (San Pablo and Suisun Bays), central 

bay, and south bay—each characterized by a central area of 

open water surrounded by intertidal mudflats and marshes (fig. 

1). Central bay includes Alcatraz and Angel Islands and also 

a number of submerged bedrock knobs that protrude through 

Shifting Shoals and Shattered Rocks—How Man Has 

Transformed the Floor of West-Central San Francisco Bay

By John L. Chin, Florence L. Wong, and Paul R. Carlson

the sediment of the bay floor and rise to within about 40 feet 

(12 m) of the water surface (fig. 2 and map supplement). The 

most prominent of these are Harding, Shag, Arch, and Blossom Rocks. These rocks have been lowered by blasting several 

times in the past, but they remain a potential hazard to shipping 

because newer cargo vessels are designed with increasingly 

deeper drafts. Central bay’s location adjacent to two major 

population and commerce centers, San Francisco and Oakland, 

subjects it to greater human influences than less developed parts 

of the estuary. The western part of central San Francisco Bay is 

adjacent to the Golden Gate, the estuary’s outlet to the Pacific 

Ocean. The changing submarine topography of the west-central 

bay, as well as its geology, form the main focus of this book.

San Francisco Bay and Its History

General Description

San Francisco Bay and its several subembayments form 

a large estuarine system. The average water depth of the San 

Francisco Bay estuary as a whole is 20 feet (6 m) mean lower 

low water (MLLW; the average height of the lower of the two 

daily low tides, used as a standard reference plane for hydrographic surveys and charts) (Conomos, 1979). The Golden Gate 

attains a maximum depth of approximately 330 feet (100 m). 

Strong tidal currents flow through the Golden Gate, sweeping 

away mud and fine sediment. This winnowing makes the floor 

of central bay generally coarser in sediment texture than the 

other bays (Rubin and McCulloch, 1979). South and north bays 

have an average depth of 10 to 13 feet (3-4 m) MLLW, with 

relatively deep tidal channels 30 to 65 feet (9-20 m) MLLW. 

Central bay in contrast has an average water depth of 36 feet 

(11 m) MLLW, about 3 times that of south and north bays. 

Because of its greater average water depth, central bay also has 

the largest water volume, even though its surface area is less 

than half that of south bay (The Bay Institute, 1998).

The Bay Ecosystem

Roughly 200 years ago, the San Francisco Bay estuarine 

system was a rich, complex, and diverse ecological habitat 

teeming with a large variety of wildlife both above and below its 

waters (The Bay Institute, 1998). Tidal marshes occupied about 
2 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Figure 1. San Francisco Bay, one of the world’s finest natural harbors, consists of three subembayments—north bay 

(San Pablo and Suisun Bays), central bay, and south bay—each characterized by a central area of open water surrounded by intertidal mudflats and marshes. This map shows the bay region as it was in the mid-1850’s, before development—areas in yellow-green along the margins of the bay are “baylands” (lands that lie between the elevations of 

high and low tides) that were present then. The population of the region has grown rapidly since the 1850’s and now 

exceeds 7 million people. The bay is an urbanized estuary, perhaps the major estuary in the United States most modified by man’s activities. This explosive development has increasingly changed the estuary and its environment. Inset 

map shows the 40 percent of California that drains through the Sacramento and San Joaquin Rivers into San Francisco 

Bay. (Modified from Goals Project, 1999; original map from Bay Area EcoAtlas 1999 San Francisco Estuary Institute.)

Central

Bay

South

Bay

North Bay N o r t h B a y

San

Pablo

Bay

Suisun

Bay

San

Jose

San

Francisco

San

Francisco

Oakland

PACIFIC OCEAN

N

Alameda

Benicia

0 10 MILES

0 10 KILOMETERS
San Francisco Bay and Its History 3

Figure 2. Bathymetric map and shaded-relief image of west-central San Francisco Bay generated from geographically corrected data obtained on 1997 U.S. Geological Survey (USGS) multibeam survey (95 kHz), with the artificial illumination from the

northwest. This image was digitally merged with a shaded-relief image for land areas derived from a USGS digital elevation model 

(DEM) having 30-m resolution. Inset shows setting of this area within central bay. Red bold lines are major bridges. Bathymetric 

contours in meters, contour interval 10 m (about 33 feet; 1 meter=3.281 feet). Red dots indicate bedrock knobs.

Red Rock

Castro

Rocks

Angel

Island

Alcatraz

Island

Treasure Yerba Island

Buena

Island

Richmond

Marin

2

1

1

2

3

3

San Francisco

Tiburon

Richmond-San Rafael Bridge

Golden Gate Bridge

San Francisco-Oakland Bay

Bridge

50

60

90

40

20

20

40

20

20

20

20

4

30

0

40

10

20

40

100

20

40

122°28' W 122°26' 122°24'

N

37°

50'

37°

52'

N

Richardson Bay

0

0 1 KILOMETER

0 1 MILE

0 1 KILOMETER

1 MILE

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Harding

Rock Shag Rock

Arch Rock

Blossom Rock

Anita Rock

Disrupted

Area

Depression

Pt Knox Shoal

Harding

Rock Shag Rock

Arch Rock

Blossom Rock

Anita Rock

Disrupted

Area

Depression

Pt Knox Shoal

Presidio Shoa

Golden l

Gate

Golden

Gate Presidio Shoal

Raccoon Strait Raccoon Strait

Alcatraz Shoal

Alcatraz Shoal

Alcatraz

Disposal

Site
4 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

200,000 acres (80,000 ha) along the bay’s margins in the early 

1800’s (Goals Project, 1999). Many of these were large contiguous tidal marshes, particularly in the north and south bays. 

Today, the tidelands (lands between high and low tides) provide 

food, shelter, and other benefits to more than 500 species of 

fish, amphibians, reptiles, birds, and mammals. If invertebrates, 

such as clams, crabs, and insects, are included, far more than 

1,000 animal species can be found in the tidelands ecosystem. 

The economic value of these tidal wetlands in the San Francisco 

Bay area alone is a major part of the annual economic value of 

wetlands for the State of California, which is estimated to be at 

least $6.3 billion (Goals Project, 1999).

San Francisco Bay is also the inland migration route for 

about 75 percent of the salmon harvested offshore California 

and for as much as 50 percent of Oregon’s catch. It supports the largest Pacific coast herring fishery south of British 

Columbia, is the nursery habitat for the Dungeness crab, and 

provides important fish habitat for other species such as English 

sole, California halibut, and striped bass (Pacific Coast Federation of Fisherman’s Associations, 1997). In the past, millions 

of birds used San Francisco Bay as part of their migration on 

the Pacific Flyway. Even now, San Francisco Bay is known as 

a major North American refuge for many species of shorebirds 

and waterfowl during their migration and wintering periods.

Figure 3. Historical changes to the bay margins in the City of San Francisco. Light purple, tidal marshlands that have 

been filled since 1847. Dark purple, open water areas filled since 1847. (Modified from Dow, 1973; base map is USGS 

San Francisco Quadrangle 1:100,000-scale topographic map, 1978 edition.)
San Francisco Bay and Its History 5

Human Influence on San Francisco Bay

San Francisco Bay has been called the “centerpiece 

of life” in the bay area—heavily interwoven with the politics, economics, social structure, and esthetics of the region 

(Kelley, 1998). To determine how man has influenced San 

Francisco Bay, both review of historical documents and direct 

observations are required. For example, a map in Dow (1973) 

reviewing historical evidence of manmade changes between 

1847 and 1972 shows the extensive alterations of the baylands 

along the northern and eastern shores of the San Francisco 

peninsula and other areas bordering central and southern San 

Francisco Bay. The waterfront acreage of San Francisco was 

increased significantly by filling tidelands and in some cases 

shallow coves and lagoons (fig. 3). Fill material included sand 

dredged from nearby Presidio Shoal, abandoned ships from 

the Gold Rush of the mid-1800’s, and debris from buildings 

that had been demolished in the 1906 earthquake. Chameau 

and others (1991) estimated that development of the San 

Francisco waterfront required more than 410 million cubic feet 

(11.7 million m3

) of fill during the period 1845 to 1920.

Although San Francisco Bay has experienced manmade 

modifications for centuries, man’s influence on the environment has increased significantly in both degree and scope over 

the past 150 years. Until the mid-1800’s, indigenous people 

and the few European settlers had minimal effect on the bay’s 

environment, but this changed with the 1848 discovery of 

gold in the foothills of the Sierra Nevada, about 100 miles to 

the northeast. The resulting Gold Rush brought about a great 

influx of people to the bay area. Many of the new immigrants 

to California arrived by boat and disembarked at ports in 

the bay, especially the burgeoning city of San Francisco. In 

1776, well before the Gold Rush, the European population of 

California numbered only about 80, but by the time of the first 

State census in 1860, that population had grown to 380,000 

(Kelley, 1998). The rapid rise in population resulting from the 

influx of miners, merchants, and other camp followers placed 

great demands on the entire watershed, including San Francisco Bay and its margins.

Modifications that have affected the floor of west-central 

San Francisco Bay include the lowering of the tops of bedrock 

knobs, dredging of harbors and waterways, filling of tidelands, artificial filling on Yerba Buena Shoal to create Treasure 

Island, dredging of sand shoals, and unintended shoaling due 

to the accumulation of Gold Rush hydraulic mining debris. 

Many of the modifications made over the past 150 years are 

essentially permanent, as natural processes or human efforts 

are unlikely to return the environment to its former state.

An example of such irreversible changes is the shoaling 

caused by the influx of hydraulic mining debris from the Sierra 

foothills (fig. 4). Hydraulic mining excavated and dislocated 

roughly 1.4 billion cubic yards (1.1 billion m3

) of material from 

ore deposits; this volume of material was 8 times that removed 

for the construction of the Panama Canal (The Bay Institute, 

1998). Gilbert (1917) estimated that enough sediment (mining 

debris) made it into San Francisco Bay by the end of the 19th 

Figure 4. The Gold Rush of the 19th century caused a population explosion in California and led to the first major manmade 

changes to the region’s landscape. This photograph shows highpressure water cannons (monitors) washing down gold-bearing gravel at the Malakoff Diggings in the foothills of the Sierra 

Nevada. Such destructive hydraulic mining methods, later outlawed in California, sent enormous quantities of sediment down 

the rivers and into San Francisco Bay, where it reduced the water 

depth over large areas. (Photograph by Carleton E. Watkins, courtesy of the Bancroft Library, University of California, Berkeley.)

century to cause the vertical accretion of tidal mudflats—3.3 feet 

(1.0 m) in Suisun Bay, 2.5 feet (0.75 m) in San Pablo Bay, and 

0.7 feet (0.25 m) in Central Bay. This influx of debris reduced 

the tidal prism (the volume of tidal flow) of the entire estuary 

and altered the tidal circulation patterns in the bay. Because vast 

quantities of hydraulic mining debris from the Gold Rush are 

still found in much of the watershed, such debris will continue to 

erode and be deposited in the estuary for a very long time.

The influx of hydraulic mining debris significantly hastened the natural sedimentation process and contributed to a permanent reduction of the open water area of San Francisco Bay 

(Nichols and others, 1986). By the 1970’s, roughly 95 percent 

of the natural wetlands in the bay and delta were lost to man’s 

activities. The Bay Institute (1998) further documents that 79 

percent of tidal marshes in the bay were reclaimed for other uses 

and 42 percent of tidal mudflats were lost to man’s activities.

The rapid expansion of commerce that accompanied 

the Gold Rush relied heavily on water-borne transport (The 

Bay Institute, 1998). Following a trend that still holds today, 

increasing maritime commerce brought about the need not 

only for more vessels but also for larger vessels of greater draft 

to handle the increasing volume of goods. Ship traffic required 

waterways where water depths were maintained at safe levels 

and hazards were removed or mitigated. In 1868, the San 

Francisco Channel, the first Federal navigation project in the 

bay, was constructed in response to this need. This project 

marked the advent of the Federal Government’s involvement 

in maritime safety issues and waterways in the estuary.

BANC PIC 1905.17175:99–ffALB
6 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

25

25

25

25

25

25

25

20

25

25

25

25

25

30

25

20

30

30

30

25

20

12

12

12

12

20

20

25

0 100 METERS

0 500 FEET

BATHYMETRIC

CONTOUR INTERVAL 1 METER

Arch Rock

Shag Rock

122°26'45" W

37°

50'

15"

N

Harding Rock

122°26'30"

37°

49'

45"

37°

50'

Figure 5. Bathymetry (water depths) over Harding, Shag, and Arch Rocks. Depths in meters corrected to MLLW (mean lower 

low water; the average height of the lower of the two daily low tides); contour interval is 1 m (1 meter=3.281 feet). Areas shallower than 20 m (66 feet) shown in brown shades. Data from 1997 U.S. Geological Survey multibeam (95 kHz) survey. 
San Francisco Bay and Its History 7

Central Bay’s Bedrock Knobs

Central San Francisco Bay is characterized by a number of 

submerged rock knobs that rise above the surrounding bay floor. 

Several of these rock knobs posed a serious hazard to navigation 

and have been lowered by blasting in the past. West-central San 

Francisco Bay in particular has several such rock knobs, some 

of which have been named—Anita, Blossom, Harding, Shag, 

and Arch Rocks (fig. 2). In addition, the emergent Red Rock 

and Castro Rocks are found in the northern part of central bay, 

near the Richmond-San Rafael Bridge. All these rock knobs in 

central San Francisco Bay are believed to be part of the same 

geological formation, the Franciscan Complex. This heterogeneous rock assemblage of Jurassic-Cretaceous age (190 to 

65 million years old) is the bedrock beneath much of the San 

Francisco Bay area (Konigsmark, 1998). Franciscan rocks form 

Yerba Buena, Angel, and Alcatraz Islands, as well as many of 

the hills of San Francisco and the Marin Headlands adjacent to 

the Golden Gate.

Harding, Shag, Arch, and Blossom Rocks all occur in a 

general northwest-southeast line that coincides with the orientation and position of Alcatraz Island (fig. 2), suggesting that they 

may be part of a continuous bedrock ridge (Carlson and others, 

2000). This structural ridge is highly irregular and trends roughly 

parallel to the Tiburon Peninsula and to other ridges in the Coast 

Range, as well as to major faults in the region (Carlson and 

others, 2000). Harding Rock rises to within about 40 feet (12 m) 

MLLW of the water surface and is characterized by three small 

individual knobs that form the shallowest part of the rock mass 

(fig. 5). According to an 1854 U.S. Coast and Geodetic Survey 

chart (Sheet no. 2, Register no. 462, “Bay of San Francisco”), 

Shag Rock then shoaled at 23 feet (7 m). The present top of Shag 

Rock is oval to rectangular in shape with two relatively flat areas, 

both at 40 feet (12 m) MLLW (fig. 5). Arch Rock is currently 

the shallowest of the rocks adjacent to Alcatraz Island, with its 

top shoaling at about 36 feet (11 m) MLLW (fig. 5). Its shape is 

somewhat rectangular and its top relatively flat. Blossom Rock 

shoals at about 40 feet (12 m) MLLW.

The likely “natural” condition of these bedrock knobs, as 

evidenced by Angel and Yerba Buena Islands and by unmodified rock knobs, such as Red Rock, is a pointed or rounded peak. 

Before it was lowered by blasting, Arch Rock projected above 

water as a sharp cone, with a large opening through it (hence 

the name) visible at low tide (fig. 6). The relatively flat top of 

Alcatraz Island is known to be a result of man’s modifications 

since the 1800’s. All the flat tops of the submerged rock knobs in 

west-central San Francisco Bay probably have a similar origin.

The increase in vessel drafts in the decades following the 

Gold Rush raised concerns about the ability of these larger 

ships to safely transit through west-central San Francisco Bay 

(Carlson and others, 2000). Blossom Rock rose to within 5 

feet (1.5 m) of the water surface at low tide in 1867 and was 

considered a hazard to safe navigation (Hagwood 1982). The 

U.S. Army Corps of Engineers (USACE) began lowering the 

top of Blossom Rock in that year and by 1870 had lowered it 

to 24 feet (7.3 m) below the water surface.

In 1898, USACE recommended that Blossom, Shag, and 

Arch Rocks be lowered to a depth of 30 feet (9 m) MLLW 

for safe navigation. Description of the work indicates that the 

two flat areas that characterize the top of Shag Rock (“Shag 

1 and Shag 2”) were blasted in 1900 (Hagwood, 1982). Arch 

Rock was blasted in 1901 (fig. 7), and work was completed in 

1902. Lowering of Blossom Rock occurred in 1902 and 1903. 

Until about 1916, USACE continued to lower the “worst” of 

the submerged rock knobs by blasting. Waterway development 

for safe navigation continued in the 1930’s. By the mid-1930’s 

Harding, Shag, and Arch Rocks had also been lowered to 36 

feet (11 m) MLLW (Hagwood, 1982).

Figure 6. Sketch of Arch Rock (with the Golden Gate in the background) around 1900, before it was blasted away as a hazard to 

navigation. The opening through the rock was visible only at low 

tide, and navigating small boats through it provided a challenge 

to daring souls. The death of one such adventurer helped seal the 

rock’s fate. (Image courtesy of U.S. Army Corps of Engineers.)

Figure 7. Blasting of Arch Rock in 1901 is seen in this photograph 

taken from San Francisco. Alcatraz Island is in the right middle 

ground. (Photograph courtesy of U.S. Army Corps of Engineers.)
8 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Studies of the Bay

Previous Work

A great number of the scientific studies documenting 

man’s impact on San Francisco Bay have focused on the biology, hydrology, and chemistry of the estuary’s waters and its 

tidelands. With the exception of Gilbert’s (1917) investigation 

of the effects of hydraulic mining debris on the watershed and 

estuary, few investigations have focused on man’s impact on and 

physical modification of the floor of San Francisco Bay. Comprehensive compilations on San Francisco Bay and its watershed 

include Gilbert (1917), Conomos (1979), Nichols and others 

(1986), The Bay Institute (1998), and Goals Project (1999). The 

adjacent tidelands, which have undergone profound modifications by man’s activities since the Gold Rush era, were studied 

by Nichols and Wright (1971), Dow (1973), and Atwater (1979), 

among many others. Investigations that at least partially deal 

with central San Francisco Bay and with man’s impact on the 

bay floor include Gilbert (1917), Carlson and McCulloch (1970), 

Carlson and others (1970), Cruickshank and Hess (1975), 

Nichols (1979), Rubin and McCulloch (1979), Chin and Clifton 

(1990), Clifton and others (1991), Chin and others (1997), Chin 

and others (1998), and Carlson and others (2000).

Recent USGS Studies of 

West-Central San Francisco Bay

Some of the major challenges specific to west-central San 

Francisco Bay include the issues surrounding potential further 

lowering of bedrock knobs (Harding, Shag, Arch, and Blossom 

Rocks), sand mining for aggregate material, and dredging for 

maintenance and improvement of waterways and harbors. All 

of these challenges are rooted in both economic and political 

issues of the San Francisco Bay region, and their resolution will 

affect the region’s overall future. Although environmental and 

regulatory policies are in place, Nichols and others (1986) noted 

that economically important issues (including deepening of ship 

channels) have in some instances been considered without sufficient scientific understanding of the effects on the estuary.

For this reason, the U.S. Geological Survey (USGS) conducted detailed studies of west-central San Francisco Bay in the 

late 1990’s. These studies revealed details of bottom features in 

the area and shed light on the natural and manmade processes 

that have influenced them, providing information essential to 

resolving the issues concerning the bay. Cooperative surveys by 

the USGS and the National Oceanic and Atmospheric Administration (NOAA) in 1997 were contracted to C&C Technologies 

(Lafayette, Louisiana). USGS surveys in 1998 and 1999 were 

Figure 8. The U.S. Geological Survey shaded-relief image of the floor of west-central 

San Francisco Bay (fig. 2) was created from data obtained in 1997 using a multibeam 

swath bathymetry system, which is a variety of sidescan sonar. In this multibeam 

system, diagramed here, a hull-mounted transducer sends sound energy 

toward the sea floor and receives back reflected sound 

through multiple narrow beams. As the ship moves 

forward (toward the lower left in the diagram), 

it maps a swath of sea floor. The record or 

image created on the shipboard recorder 

has the ship’s direction as one axis and the 

distance between the transducer and the 

bottom (“slant range”) as the other axis. 

Strong returned signals (“high backscatter”) 

form dark areas on the image; weak signals 

(“low backscatter”) form light areas. The first 

signal returned is from directly below the 

ship, and its slant range is equal to the water 

depth below the transducer. Traditional sidescan-sonar systems produce similar images 

(see figs. 13 and 15-18), but because the 

transducer is towed behind the ship, data are 

not precisely referenced as to location and water depth. Uncorrected images produced by any sidescan-sonar system contain distortions of scale 

and shape, both because of variations in the ship’s forward speed and because of the 

varying angles of the slant-range distances. Image-processing software can remove 

these distortions and produce a geographically correct image, such as that in figure 

2. The 1997 survey was operated from the C&C Technologies vessel Coastal Surveyor 

(seen in the inset photograph with the semicircular multibeam sound transducer 

raised above water—during operations the transducer is lowered into the water).
Areas and Issues of West-Central San Francisco Bay 9

done using the research vessel RV David Johnston. Navigation on all surveys was based on differential global positioning 

systems (DGPS). The nominal horizontal accuracy obtained 

using DGPS was on the order of 3 feet (1 m). Vertical accuracy 

of acoustic data was 0.3 to 0.6 feet (0.1-0.2 m).

Acoustic data were obtained with two different instrument systems. On the 1997 surveys, a Simrad EM-1000 

multibeam swath bathymetry system was used to image the 

bay floor (fig. 8). Approximately 17.5 square miles (45 km2

) 

of the bay floor was imaged using the multibeam system. 

This system simultaneously acquired spatially coregistered 

bathymetric and backscatter data at a frequency of 95 kHz. 

Tracklines were run with 100 percent overlap so as to produce 

a continuous mosaic of the area (fig. 2).

A Klein sidescan-sonar system was used on the 1998 and 

1999 surveys to obtain acoustic imagery. The Klein sidescansonar imagery was collected to field check observations and 

interpretations that had been made from the 1997 multibeam 

data. The operating frequency of the sidescan system was 100 

kHz, with a range of 330 feet (100 m).

Areas and Issues of West-Central San 

Francisco Bay

West-central San Francisco Bay, as shown by a USGS 

shaded-relief image generated from data collected on a 1997 

survey (fig. 2), is the deepest part of the bay and is characSan Francisco

Limit

of data

PACIFIC OCEAN

Tiburon

Peninsula

Marin

Peninsula

Richmond

N

Treasure

Island

Alcatraz

Island

Angel

Island

Flat beds, bedrock,

and boulders

Bedforms less than

1 meter in height

Bedforms between 1

and 3 meters in height

Bedforms greater

than 3 meters in height

EXPLANATION

0 1 M

0 1 KM

terized by the coarsest sediment in the entire estuary. The 

bay floor is molded into a variety of topographic features 

(bedforms) that are the result of the interaction of sediment, 

tidal currents, and water depth, as well as the influence of 

human activities.

USGS scientists Rubin and McCulloch (1979) documented naturally occurring bedforms and bottom types in 

central San Francisco Bay using sidescan-sonar imagery (100 

kHz frequency). They delineated three basic bottom types in 

the central bay—bedforms (in three size ranges), “flat beds,” 

and bedrock or boulders (fig. 9).

The bedforms consist primarily of sand waves (if ripples 

were present, their size was below the 0.3- to 0.6-foot (0.1-0.2 

m) resolution limit of the sidescan-sonar system used). The 

sand waves were subdivided into three classes on the basis of 

their heights—less than 3 feet (1 m), 3 to 10 feet (1-3 m), and 

greater than 10 feet (3 m) (fig. 9). Sand waves covered roughly 

half of the area surveyed in central bay in 1979.

The second most abundant bottom type mapped in 1979 

in central bay was “flat beds,” areas that appear flat in sidescan 

imagery because any irregularities were less than 0.3 feet (0.1 

m) high, below the resolution limit of the sidescan system. Flat 

beds included both areas of relatively smooth sediment cover 

and flat areas of exposed bedrock.

The third bottom type, bedrock and boulders, was mapped 

primarily in the vicinity of the Golden Gate. In this area, the bay 

floor is continually swept clear of sediment by high-velocity 

tidal currents, keeping boulders and rock exposed.

Rubin and McCulloch’s (1979) map of bay-floor bottom 

types of central San Francisco Bay provides a baseline for 

detecting subsequent changes in bottom types and features 

resulting from man’s activities. The map encompasses the 

entire area that was later surveyed by the USGS in the 1990’s 

and is the subject of this paper. These USGS studies focused 

on several areas and issues of west-central San Francisco Bay, 

including Point Knox Shoal, Presidio Shoal, bedrock knobs, 

the Alcatraz Disposal Site, and dredging.

Point Knox Shoal

Point Knox Shoal forms an arcuate submerged topographic 

high extending to the southwest from Angel Island between 

Points Stuart, Knox, and Blunt (fig. 2). Water depths over the 

shoal range from about 20 to 65 feet (6-20 m). The southeastern 

margin of the shoal is characterized by sand waves that trend 

approximately north-south and are roughly 3 to 6 feet (1-2 m) in 

height with a wavelength of 100 to 200 feet (30-60 m). At their 

Figure 9. Sidescan-sonar surveys in the 1970’s delineated areas 

of the bottom in west-central San Francisco Bay characterized 

by bedrock, boulders, flat sediment, and bedforms. Bedforms are 

mainly sand waves and dunes. Red lines are bridges—see figure 

2. (Map modified from Rubin and McCulloch, 1979.)
10 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Figure 10. Shaded-relief image of west-central San Francisco Bay (see fig. 2), showing borrow areas used during 1936–38 to provide dredged material for constructing Treasure Island. Note that the topographic depression in the present bay floor southwest of 

Angel Island largely coincides with the western part of the 1936–38 borrow site on Point Knox Shoal. (Multibeam shaded-relief image 

of bay floor by U.S. Geological Survey, 1997; borrow areas from Cruickshank and Hess, 1975.)

1936-38

Pt Knox Shoal

borrow area

1

122°28' W 122°26' 122°24'

37°

50'

37°

52'

N

N

1936-38

Pt Knox Shoal

borrow area

Richardson Bay

Topographic

depression

Harding

Rock Shag Rock

Arch Rock

Blossom Rock

Anita Rock

Harding

Rock Shag Rock

Arch Rock

Blossom Rock

Anita Rock

Presidio/Alcatraz Shoal residio/Alcatraz Shoal

Golden

Gate

Golden

Gate

Raccoon Strait Raccoon Strait

Topographic

depression

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Red Rock

Castro

Rocks

Angel

Island

Alcatraz

Island

Treasure Yerba Island

Buena

Island

Richmond

Marin

2

1

1

2

3

3

San Francisco

Tiburon

Richmond-San Rafael Bridge

Golden Gate Bridge

San Francisco-Oakland Bay

Bridge

0

0 1 KILOMETER

1 MILE
Areas and Issues of West-Central San Francisco Bay 11

southwesternmost limit, the sand waves appear to merge with 

another field of sand waves that covers the northeast flank of 

Harding Rock (fig. 2). Much of the surface of Point Knox Shoal 

is covered by small sand waves less than 3 feet (1 m) in height 

and of variable orientation. The southwesternmost part of the 

shoal is characterized by a zone of irregular to linear depressions with intervening highs. The USGS multibeam sonar image 

of this part of the shoal yields an impression of intense disruption and a chaotic fabric (fig. 2). The area on Point Knox Shoal 

typified by this chaotic fabric covers 0.35 square mile (0.9 km2

). 

The part of the shoal between this chaotic zone and Points Stuart and Knox on Angel Island is topographically lower than the 

surrounding shoal (fig. 2). This topographic depression covers 

0.3 square mile (0.8 km2

) and trends northeast-southwest. It is 

separated from the deeper Raccoon Strait by a submerged sediment ridge. Much of the floor of the depression occurs under 50 

to 60 feet (15-18 m) of water.

Bathymetric maps from the 1800’s and early 1900’s are 

not sufficiently detailed to show whether the disrupted zone 

and the topographic depression existed on Point Knox Shoal 

in those times. However, there is reason to believe that these 

areas on Point Knox Shoal have been greatly modified by 

more recent dredging activities.

Origin of the Topographic Depression on 

Point Knox Shoal

Day (1938), Scheffauer (1954), and Cruickshank and 

Hess (1975) document that the area southwest of Angel Island, 

including much of Point Knox Shoal, was used as a borrow 

pit and sand-mining area during 1936–1938 for construction 

fill (fig. 10). This fill material was used to create Treasure 

Island on a shoal northwest of Yerba Buena Island for the 1939 

Golden Gate International Exposition (fig. 11). There is no 

record of the specific volume of material excavated from Point 

Knox Shoal, nor of the exact sites from which it was removed 

on the shoal. However, Scheffauer (1954) reported 20 to 29 

million cubic yards (15.3-22.2 million m3

) as the total volume 

removed from both Point Knox Shoal and Alcatraz/Presidio 

Shoal to create Treasure Island. Hopper dredges were the 

common equipment used to excavate the sand for construction 

fill (Scheffauer, 1954; Cruickshank and Hess, 1975). A hopper 

dredge deploys a dragarm over the side of a barge and uses 

suction to extract sand from the sea floor. The dragarm and its 

draghead are only capable of skimming the sea-floor surface 

and provide minimal penetration (less than 3 feet or 1 m).

A plot of the location of the 1939 Golden Gate International Exposition dredging site on Point Knox Shoal projected 

onto USGS multibeam imagery reveals that most of the 

topographic depression on Point Knox Shoal coincides with 

the westernmost portion of the 1936–1938 dredging site (fig. 

10). The volume of material removed from the topographic 

depression on Point Knox Shoal was estimated by geometrically draping a flat surface over the depression. The resulting estimate of 3.1 million cubic yards (2.4 million m3

) is a 

reasonable minimum figure considering the estimates cited by 

Figure 11. Aerial photograph of 

Treasure Island and the 1939 Golden 

Gate International Exposition. 

Treasure Island was built up entirely 

by filling in a shallow area of San 

Francisco Bay north of Yerba Buena 

Island (right). The eastern half of the 

San Francisco-Oakland Bay Bridge 

in the background leads to Oakland 

and the East Bay. The Golden Gate 

International Exposition celebrated 

the completion of the Bay Bridge in 

1936 and the Golden Gate Bridge in 

1937. Part of Treasure Island served 

as Pan American Airways’ seaplane 

terminal for its trans-Pacific Clipper service (below right), and the 

intention was that after the close of the Exposition in 1940, Treasure 

Island would become an international airport for San Francisco. 

However, in World War II the U.S. Navy took over the island, and 

San Francisco had to build its international airport elsewhere. (Photographs courtesy of the San Francisco Museum history collection.)
12 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Scheffauer (1954) for the total volume of sediment removed 

from both Point Knox and Alcatraz/Presidio Shoals.

The depression in Point Knox Shoal appears to be too 

deep and extensive to have been dredged solely by hopper 

dredges, which at each pass typically can excavate an elongate 

depression only 3 to 6 feet (1-2 m) wide and less than 3 feet (1 

m) deep. A dredge with the capacity to excavate more deeply 

into the substrate was probably used on Point Knox Shoal in 

addition to or subsequent to the 1936–1938 dredging by hopper dredges. For example, a stationary dredge is capable of 

excavating the substrate to a depth of at least 30 to 50 feet (10-

15 m) (deGroot, 1979). The topographic depression in Point 

Knox Shoal is similar to a borrow area in South San Francisco 

Bay adjacent to Bay Farm and Alameda Islands (fig. 12). This 

borrow area encompassed roughly 50 million square feet (4.7 

million m2) and served as a source of sediment for construction fill on Bay Farm Island. It likely was excavated by a 

stationary dredge, and in places was 26 to 33 feet (8-10 m) 

Figure 12. Bathymetric profile and 

map of borrow area 

set aside for dredging of fill material in 

San Francisco Bay 

adjacent to Bay 

Farm and Alameda 

Islands. This borrow area encompassed roughly 5.6 

million square yards 

(4.7 million m2

) and 

served as a source 

of sediment for construction fill on Bay 

Farm Island. It likely 

was excavated by 

a stationary dredge 

and in places was 

26 to 33 feet (8-10 

m) deeper than the 

surrounding area. 

(U.S. Geological 

Survey data collected in 1985 using 

200-kHz sonar.)

MEAN SEA LEVEL

-5

-10

-15

Alignment of 1985

bathymetry profile

San Francisco Bay

Borrow

Area

Alameda

Ballena

Bay

Borrow Area

Crib line

pilings

A A'

A

A'

DEPTH, IN METERS

San Leandro Channel

0

0 1 KILOMETER

1 MILE

0 200 METERS (656 FEET) VERTICAL EXAGGERATION X 30

SAN N

FRANCISCO

Area of

Fig 12 SAN FRANCISCO BAY

Bay

Farm

Island

deeper than the surrounding bay floor (National Ocean Survey 

chart no.18650, 1980 edition).

The Point Knox Shoal topographic depression occurs 

within the boundaries of an active sand mining lease area 

designated “PRC-709.1 North” by the California State Lands 

Commission (CSLC). The USGS multibeam imagery from 

1997 (fig. 2) revealed that the floor of the depression is covered 

by small natural sand waves, 0.3 to 3 feet (0.1-1 m) in height, 

with a diverse mix of orientations. No apparent signs of recent 

dredging were seen within the topographic depression.

There may have been a depression on Point Knox Shoal 

even before dredging occurred there. The depression occurs offshore of two prominent topographic features, Points Knox and 

Stuart on Angel Island (fig. 2). Natural topographic depressions 

occur offshore of Points Blunt and Campbell on Angel Island 

and offshore of the Belvedere Peninsula (fig. 2). A disposal site 

southwest of Alcatraz Island used for materials dredged from 

shipping channels in the bay (fig. 2) was, in the 1800’s, a topo-
Areas and Issues of West-Central San Francisco Bay 13

feet (16-24 m). On 100-kHz sidescan-sonar images, the chaotic 

fabric is a composite of closely spaced circular, semicircular, 

and elongate depressions with intervening higher areas (fig. 13). 

These depressions and their intervening highs are so numerous 

over a relatively small area that they appear to interlace.

The circular to semicircular depressions range in size 

from 6 to 26 feet (2-8 m) wide and from 6 to 65 feet (2-20 

m) long and occur both individually and in clusters (fig. 13). 

Many of these depressions are characterized by a raised rim 3 

to 6 feet (1-2 m) high, typically on one side only.

Elongate depressions (or troughs), from linear to curvilinear in shape, appear to be more numerous than the circular 

depressions within the disrupted zone on Point Knox Shoal. 

These troughs are commonly 6 to 33 feet (2-10 m) wide, 33 

to 200 feet (10-60 m) long, and 3 to 10 feet (1-3 m) deep as 

measured using 100-kHz sidescan sonar (fig. 13). The troughs, 

like the circular depressions, also commonly feature a flanking 

rim that parallels one side and rises 3 to 6 feet (1-2 m) above 

Figure 13. U.S. 

Geological Survey 

sidescan-sonar 

image (100 kHz; 

uncorrected) 

collected in January 1998 showing 

dredge-related 

features in the 

disturbed zone on 

Point Knox Shoal. 

Features visible in 

this image include 

elongate troughs 

(depressions), rims, 

and circular to semicircular depressions. 

Compare this to figure 15. (For explanations of slant-range 

scale and light and 

dark areas in image, 

see figure 8.)

0 100 METERS (328 FEET)

0

20

20

40

60

80

40

60

80

100

100

Rim

Elongate depression

Circular to semicircular

depressions

SLANT RANGE, IN METERS

SW Ship's track NE

graphic depression 165 feet (50 m) below the adjacent bay floor 

(U. S. Environmental Protection Agency, 1996). In central San 

Francisco Bay there appears to be a clear correlation between 

submerged topographic depressions and prominent adjacent 

onshore topographic features such as points, headlands, and 

islands. Once a depression is formed in the bay floor, tidal currents appear to maintain that topographic feature as a depression 

by inhibiting sedimentation or by causing erosion.

The Disrupted Zone on Point Knox Shoal

The appearance of the southwestern part of Point Knox 

Shoal is distinct from any other part of the floor of west-central 

San Francisco Bay imaged by the USGS in 1997 (fig. 2; Chin 

and others, 1997, 1998). A thoroughly chaotic and intensively 

disturbed fabric characterizes this part of the shoal, in contrast 

to the relatively smooth fabric of the adjacent topographic 

depression. This disturbed zone is at a water depth of 52 to 78 
14 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

the flank of the trough. Troughs may occur adjacent to or 

distinct from circular depressions. On sidescan-sonar images 

(both 95 and 100 kHz), troughs appear to cross one another, 

sometimes several times.

Previous surveys by Rubin and McCulloch (1979) 

and Chin and Clifton (1990) of central San Francisco Bay, 

based largely on nonoverlapping reconnaissance-style 

sidescan-sonar coverage (100 kHz), did not reveal any 

extensive zones of bay floor with chaotic or disrupted fabric. However, analysis of original sidescan-sonar images 

from the Rubin and McCulloch (1979) survey showed that 

similar circular to semicircular and elongate depressions 

did exist in the same area on Point Knox Shoal. The number and density of depressions appear to have been much 

less than in the 1997 survey, possibly because of the fewer 

number of transects available. The only area of bay floor 

remotely similar to this disrupted zone occurs on Presidio 

Shoal, just north of the San Francisco waterfront, and is 

discussed below.

Several lines of evidence indicate that the disrupted 

zone on Point Knox Shoal is largely due to dredging. 

Furthermore, in contrast to the topographic depression on 

the shoal, probably created by decades-old dredging, the 

disrupted zone is thought to be the result of more recent 

dredging activities. The disrupted zone largely occurs outside of the 1936–1938 borrow area (fig. 10).

Today, sand-and-gravel aggregate mining companies 

that hold leases granted by CSLC are allowed to extract 

sand from the bay floor. The leases are monitored by 

CSLC, San Francisco Bay Conservation and Development 

Commission (BCDC), and USACE, the regulatory agencies responsible for overseeing present-day sand mining 

on submerged State lands. A map of current lease areas 

provided by CSLC (fig. 14) shows that lease areas PRC 

709.1 North and PRC 2036 include the disrupted zone of 

Point Knox Shoal. Lease area PRC 7779 is adjacent to PRC 

2036 and extends to the southwest; this lease area includes 

the periphery of Point Knox Shoal (fig. 14).

During the January 1999 USGS cruise in west-central 

San Francisco Bay, hopper dredges were observed over a 

2-day period mining sand on Alcatraz, Presidio, and Point 

Knox Shoals. The positions of the sand-mining dredges were 

fixed using DGPS. Later, after the dredges left the area, the 

USGS ran 100-kHz sidescan-sonar transects on Point Knox 

Shoal to examine bed features caused by the dredging. Figure 15 shows features on the shoal probably created by the 

dredging—circular to semicircular and elongate depressions, 

all of them unfilled and clearly recent in origin.

Bed features within the heart of the disrupted zone 

on Point Knox Shoal are so numerous, closely spaced, and 

interwoven that it is hard to distinguish individual features. 

Therefore, similar features found around the periphery of the 

disrupted zone are the key to deciphering their origin. Figure 

16 shows bed features on the disrupted zone periphery as 

seen on the USGS 1997 multibeam base map. Individual and 

distinct linear to curvilinear elongate depressions (troughs) 

are present, some intersecting and crossing each other. These 

bed features are clearly very similar to the features observed 

just after hopper dredges mined the bay floor in 1999 (fig. 

15). Because of this, all the circular to semicircular and 

elongate depressions found in the disrupted zone are interpreted to be the result of hopper-dredge sand mining. The 

circular to semicircular depressions, sometimes observed 

in a curving progression, are probably caused by the hopper dredge’s trailing suction-arm draghead encountering the 

bay floor discontinuously. In a number of sidescan-sonar 

examples, a succession of pits was observed that led into an 

elongate trough. According to Scheffauer (1954), once a hopper dredge operator has determined that sand being extracted 

is suitable, the dredge barge is slowly moved forward with 

the dragarm trailing behind it and the draghead in contact 

with the bottom. The elongate trough, therefore, probably 

represents bay floor where the dragarm was left on the bed 

continuously to extract sand.

Close examination of figure 16 reveals that there is a 

subtle north-south grain present within the disrupted zone 

on Point Knox Shoal. Further examination of areas and 

bay-floor types adjacent to the disrupted zone shows that 

sand waves (generally more than 3 feet—1 m—in height) 

on the southeast flank of Point Knox Shoal and also in 

other areas of west-central San Francisco Bay exhibit an 

approximate north-south orientation. The subtle northsouth grain observed in the disrupted zone may represent 

the remnants of former sand waves, similar to those on 

the southeast flank of Point Knox Shoal and on Alcatraz/

Presidio Shoal. If so, sand mining activities within the 

disrupted zone have been so intensive that the sand waves 

are mostly obliterated.

Presidio Shoal

Presidio Shoal is part of a submerged shoal complex, 

including Alcatraz Shoal, that extends southwest from Alcatraz Island toward the Golden Gate (fig. 2). The two shoals 

are contiguous, with Alcatraz Shoal to the northeast and Presidio Shoal to the southwest. Water depths range from 36 to 

60 feet (11-18 m) over Alcatraz Shoal and from 50 to 75 feet 

(15-23 m) over Presidio Shoal. The surfaces of both shoals 

are covered by prominent sand waves (fig. 2). The sand 

waves are approximately 3 to 6 feet (1-2 m) in height and 

have wavelengths ranging from about 80 to 290 feet (25-90 

m). The orientation of the sand waves is mostly north-south, 

varying to northnortheast-southsouthwest. On the southern 

margin of Presidio Shoal, just north of the San Francisco 

waterfront, the large 3- to 6-foot (1-2 m) sand waves appear 

to fade, and the bay floor is typified by smaller sand waves 

(generally less than 3 feet—1 m—high) and by circular 

depressions that occur singly and in clusters.

The Marina District of San Francisco, adjacent to the 

southern margin of Presidio Shoal (fig. 3), has undergone significant modifications since about the mid-1800’s. Dow (1973) 

and Bonilla (1991) documented extensive filling and alteration 
Areas and Issues of West-Central San Francisco Bay 15

Red Rock

Castro

Rocks

Angel

Island

Alcatraz

Island

Treasure Yerba Island

Buena

Island

Richmond

Marin

2

1

1

2

3

3

San Francisco

Tiburon

Richmond-San Rafael Bridge

Golden Gate Bridge

San Francisco-Oakland Bay

Bridge

122°28' W 122°26' 122°24'

N

37°

50'

37°

52'

N

Richardson Bay

0

0 1 KILOMETER

0 1 MILE

0 1 KILOMETER

1 MILE

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Harding

Rock Shag

Rock

Arch

Rock

Blossom Rock

Anita Rock

Pt Knox Shoal

Presidio Shoal

Harding

Rock

Shag

Rock

Arch

Rock

Blossom Rock

Anita Rock

Golden

Gate

Golden

Gate

Pt Knox Shoal

Presidio Shoal

Raccoon Strait Raccoon Strait

Alcatraz Shoal Alcatraz Shoal

PRC 709

South PRC 7780

South

PRC 5871

PRC 709.1 East

PRC

PRC 7780 7779

West

PRC 7779

North

PRC 709.1

North

PRC 2036

PRC 7779

East

PRC 709

South PRC 7780

South

PRC 5871

PRC 709.1 East

PRC

PRC 7779 7780

West

PRC 7779

North

PRC 709.1

North

PRC 2036

PRC 7779

East

Figure 14. Approximate locations of lease areas for sand extraction in west-central San Francisco Bay as of June 1999, based on data 

from the California State Lands Commission (CSLC) Boundary Unit. Base map is composed of USGS shaded-relief images (see fig. 2).
16 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

0

20

20

40

40

60

60

80

80

Rim

Elongate

depression

Irregular

depressions

Crossed

depressions

Crossed

depressions

SLANT RANGE, IN METERS

Ship's track

0 100 METERS (328 FEET)

Figure 15. U.S. Geological Survey sidescan-sonar image (100 kHz; uncorrected) of recent dredge-related 

features on Point Knox Shoal collected in January 1999, shortly after a hopper dredge was observed operating 

over this part of the shoal. Note that elongate depressions cross each other several times. Compare this figure 

to figure 13. (For explanations of slant-range scale and light and dark areas in image, see figure 8.)

of this area. A shallow cove was located at the site of the present Marina District in 1851 (Bonilla, 1991). The greatest water 

depth within the cove was about 16 feet (5 m) MLLW. This 

cove existed until early 1912, when sediment was excavated 

from the southernmost edge of Presidio Shoal with suction 

dredges to create the fairgrounds for the 1915 Panama-Pacific 

Exposition (Bonilla, 1991). Markwart (1915) reports that from 

1912 to 1915 approximately 1.3 to 2 million cubic yards (1-1.5 

million m3) of sediment (70 percent sand, 30 percent mud) was 

excavated from Presidio Shoal for the exposition.

Presidio Shoal was also part of a designated borrow 

site (fig. 10) for the 1939 Golden Gate Exposition (Scheffauer, 1954; Cruickschank and Hess, 1975; Hagwood, 

1982). Hopper dredges were used to extract an indeterminate amount of sand from the shoal from 1936 to 1938.

At present, Presidio Shoal is part of an active sandmining lease, designated PRC-709 South (fig. 14) by the 

CSLC. Additionally, most of Alcatraz Shoal is covered by 

three active lease sites, PRC-5871, PRC-709.1 East, and 

PRC-7780 South (fig. 14).

Almost all of the circular, semicircular, and elongate 

depressions on Presidio Shoal occur within the boundaries 

of PRC-709 South. These features on the southern margin 

of Presidio Shoal are broadly similar to the features in 
Areas and Issues of West-Central San Francisco Bay 17

Figure 16. Elongate and circular to semicircular depressions 

(within outlined areas) on the periphery of the Point Knox 

Shoal disrupted zone. Image is an enlarged portion of the 

USGS shaded-relief image of west-central San Francisco Bay 

generated from the 1997 multibeam survey (see fig. 2). High 

backscatter appears dark, low backscatter appears light (for 

explanation, see figure 8). Note the similarity of these features 

to those shown in figures 13, 15, and 17.

the disrupted zone on the southwestern tip of Point Knox 

Shoal. Both sets of bottom features occur within present day sand-mining lease sites, and hopper dredges were 

observed mining sediment at each site during field surveys 

by USGS scientists in January 1999. After observing sand 

mining on Presidio Shoal, the USGS conducted a 100-

kHz sidescan-sonar survey of the dredge site. The features 

imaged were fresh and similar to those acquired on Point 

Knox Shoal after the passage of a sand-mining dredge. 

Circular and semicircular depressions on the images were 6 

to 13 feet (2-4 m) in width, and elongate depressions were 

about 6 feet (2 m) in width and 65 to 250 feet (20-75 m) in 

length (fig. 17). As was also observed on Point Knox Shoal, 

both circular and elongate depressions have a flanking rim 

raised above one edge, and a number of elongate depressions cross each other. These manmade bottom features 

clearly cut across natural sand waves (fig. 17). The elongate 

depressions observed on 100-kHz sidescan-sonar images on 

Presidio Shoal after sand mining in 1999 were not evident 

on USGS 95-kHz multibeam imagery from 1997. They may 

have been below the resolution of the multibeam system, 

or absent at the time of the 1997 survey. No sand-mining 

dredges were observed on west-central San Francisco Bay 

during the 1997 survey.
18 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

0

20

20

40

40

60

60

80

80

0 100 METERS (328 FEET)

"Turn"

Crossing

elongate

depressions

Raised rim

Raised rim

Elongate

depression

"Test pits"

with rims

Irregular

depression

SLANT RANGE, IN METERS

Elongate

depression

Ship's track

Figure 17. U.S. Geological Survey sidescan-sonar image (100 kHz; uncorrected) of recent dredge-related features on 

Presidio Shoal collected in January 1999, shortly after a hopper dredge was observed operating over this part of the shoal. 

The dredge-related features cut across natural sand waves (the light and dark stripes in the lower part of the image), and 

some of the elongate depressions cross over each other several times. Note the similarity of these dredged features to 

those in figures 13, 15, and 16. (For explanations of slant-range scale and light and dark areas in image, see figure 8.)

Bedrock Knobs

In January 1999, the USGS collected underwater video over 

Harding, Arch, and Shag Rocks to verify interpretations made 

from sidescan sonar (J.L. Chin and P.R. Carlson, unpub. data, 

2000). As shown on the sonar images, the top of Shag Rock is 

strewn with rocky rubble and debris of all sizes and shapes (fig. 

18). The size of rubble ranges from cobbles to large boulders 

several meters across. A large amount of the rock debris is angular. Some rock appears to be in place, but mostly the underwater 

video showed blocky rubble scattered over the surface of Shag 

Rock. Similarly, the surfaces of Harding Rock and Arch Rock are 

strewn with rocky debris of all shapes and sizes from cobbles to 

boulders. Such debris is consistent with what would be expected 

for rock masses that had been blasted. A fair amount of rubble 

from blasting was evidently left in place on the rock knobs.

Available records indicate that the tops of these rock 

knobs in west-central San Francisco Bay have not been 
Areas and Issues of West-Central San Francisco Bay 19

Figure 18. U.S. Geological Survey sidescan-sonar image (100 kHz; uncorrected) over Shag Rock collected in January 

1999, showing the rocky debris that covers its surface. The debris includes boulders and blocky rubble of various sizes 

and shapes. On upper left side of figure are sand waves that terminate against the flank of Shag Rock. (For explanations of 

slant-range scale and light and dark areas in image, see figure 8.)

0 100 METERS (328 FEET)

0

20

40

60

80

20

40

60

80

Blocky debris Ship's track

SLANT RANGE, IN METERS

lowered artificially since the mid-1930’s. Their present 

depths below the water surface are therefore suited to vessels 

with drafts typical of the first half of the twentieth century, 

making them a navigational hazard to the modern deep-draft 

vessels that now transit through west-central San Francisco 

Bay (fig. 19). Another factor that makes these rock knobs a 

potential hazard to safe navigation is that the navigation traffic 

lanes that vessels take into and out of San Francisco Bay have 

changed since the knobs were last lowered. At present, Harding, Shag, and Arch Rocks lie within the westbound vesseltraffic lane (fig. 20). Blossom Rock (as well as the Alcatraz 

Disposal Site) is within the eastbound vessel-traffic lane. In 

addition, Harding Rock is within about 1,000 feet (300 m) of 

the two-way deep-draft vessel traffic lane (fig. 20).

Ports immediately adjacent to west-central bay include the 

Port of San Francisco, the Port of Richmond, and the Port of 

Oakland. Vessels that use the Port of Oakland are dominantly 

container vessels (fig. 21), whereas those using the Port of 
20 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Figure 19. The evolution of vessel draft through time. Image at far left represents a sailing ship from the Gold Rush era; the other 

images show successive generations of ever-larger container ships. The evolution of oil tankers has paralleled that of container vessels, with increasing vessel size and draft over time. The bedrock knobs in San Francisco Bay that were artificially lowered to about 40 

feet below mean sea level in the first half of the 20th century are clearly once again a potential hazard to the largest vessel (see fig. 20). 

Diagram modified from Pisani (1989); original schematic copyright by Port of Oakland, September 1989.

Richmond are oil tankers (fig. 22). An assortment of vessels, 

including passenger liners, call at the Port of San Francisco (San 

Francisco Bay Conservation and Development Commission and 

Oakland Metropolitan Transportation Commission, 1996). At the 

time the bedrock knobs were last lowered in the mid-1930’s, the 

deepest draft vessels were steamships with 23-foot (7 m) drafts 

which required that the tops of the bedrock knobs be approximately 26 feet (8 m) MLLW. However, modern deeper draft 

vessels are now rapidly replacing smaller older vessels (fig. 19). 

The latest generation of container vessels are as much as 1,300 

feet (396 m) long, 150 feet (46 m) wide, and have drafts of 46 to 

50 feet (14-15 m). These container vessels often carry as many as 

5,000 “twenty-foot equivalent unit” (TEU) containers (San Francisco Bay Conservation and Development Commission and Oakland Metropolitan Transportation Commission, 1996). Larger, 

deeper draft vessels are more efficient and thus more cost effective, both to their owners and to ports. This trend toward larger, 

more cost-effective vessels is true not only for container vessels 

but also for oil tankers and passenger liners—transporting oil in a 

50,000-ton tanker costs twice as much as in a 300,000-ton tanker 

over a 25,000-mile transit (Herbich, 2000).

Between 1988 and 1993 the annual number of ships visiting San Francisco Bay actually decreased by almost 300, while 

the volume of cargo coming into the bay increased. This trend is 

likely to continue as fewer but larger cargo and passenger vessels call in the bay. It is forecast that maritime cargo transiting 

San Francisco Bay will more than triple by the year 2020 (San 

Francisco Bay Conservation and Development Commission and 

Oakland Metropolitan Transportation Commission, 1996).

After the U.S. Congress proposed lowering the tops of the 

bedrock knobs in west-central San Francisco Bay to remove 

the potential hazard to navigation for deep-draft vessels 

(Carlson and others, 2000), the U.S. Army Corps of Engineers 

undertook a feasibility study in 2000. Earlier cost estimates for 

such a project ranged from 10 to 43 million dollars (Rogers, 

1996), but in their recent feasibility study, USACE estimated 

the costs at more than $200 million. USACE concluded that 

the benefits of lowering the bedrock knobs would not offset 

these high costs, because current navigation practices make an 

oil spill resulting from a tanker or other vessel grounding on 

one of the knobs very unlikely (U.S. Army Corps of Engineers, 2003). However, it is worth noting that the economic 

losses from the 1989 T/V Exxon Valdez oil spill in Prince William Sound, Alaska, are at least $2.8 billion (State of Alaska, 

unpub. information accessed online on March 11, 2004, at 

http://www.evostc.state.ak.us/facts/economic.html). In addition, USACE was not asked in their recent study to consider 

the possible effects of spills of other kinds of toxic materials 

resulting from vessel groundings on the knobs.

Both environmentally and economically there is much at 

stake for the San Francisco Bay region. The Port of Oakland is 

the fourth largest port for containerized shipping in the United 

States and the third largest container port on the U.S. West 

Coast. San Francisco Bay is one of the three primary Pacific 

coast gateways for U.S. containerized cargoes; the others are 

San Pedro Bay and Puget Sound. At present 98 percent of the 

containerized goods arriving in the San Francisco Bay region, 

the nation’s fourth largest metropolitan area, is discharged at 

the Port of Oakland. Additionally, California is the Nation’s 

leading agricultural state, and many California agricultural 

products are exported through the Port of Oakland. The Port 

of Oakland currently has $700 million in maritime projects 

under construction or in planning (Port of Oakland, Facts and 

Figures, unpub. data accessed online November 29, 2000 at 

http://www.portofoakland.com/maritime/index.html). The port 

was directly responsible for 9,600 jobs in 2000; this figure 

EVOLUTION OF CONTAINER SHIPS

Pre1960

1971-80 1981-90 1988-95 1990-2000 1998-

< 30 ft

(<9.1 m)

Present tops of

Harding, Shag, and Arch Rocks

33 ft

(10 m) 38-41 ft

(11.6-12.5 m)

38-42 ft

(11.6-12.8 m) 42-46 ft

(12.8-14 m)

>46 ft

(>14 m)

DRAFT, IN FEET (METERS)

MEAN SEA LEVEL

-20 ft (-6 m)

-40 ft (-12.2 m)
Areas and Issues of West-Central San Francisco Bay 21

20

20

40

30

50

10

60

90

40

20

40

100

40

20

20

20

40

20

40

20

122°28' W 122°26' 122°24'

N

37°

50'

37°

52'

N

Richardson Bay

0

0 1 KILOMETER

0 1 MILE

0 1 KILOMETER

1 MILE

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Tiburon Peninsula

Sausalito

Angel

Island

San Francisco

Alcatraz Island

Pt Blunt

Pt Knox

Pt Stuart

Marin Peninsula

Belvedere Peninsula

Harding

Rock

Shag Rock

Arch Rock

Blossom Rock

Anita Rock

Disrupted

Area

Depression

Pt Knox Shoal

Harding

Rock

Shag Rock

Arch Rock

Blossom Rock

Anita Rock

Disrupted

Area

Depression

Pt Knox Shoal

Alcatraz

Disposal

Site

Presidio Shoa

Golden l

Gate

Golden

Gate Presidio Shoal

Alcatraz Shoal Alcatraz Shoal

Raccoon Strait Raccoon Strait

Red Rock

Castro

Rocks

Angel

Island

Alcatraz

Island

Treasure Yerba Island

Buena

Island

Richmond

Marin

2

1

1

2

3

3

San Francisco

Tiburon

Richmond-San Rafael Bridge

Golden Gate Bridge

San Francisco-Oakland Bay

Bridge

Figure 20. Traffic lanes for large vessels (1,600 gross tons or greater) in west-central San Francisco Bay, as designated by the 

U.S. Coast Guard’s Vessel Traffic Service San Francisco (more information at http://www.uscg.mil/D11/vtssf). Lane boundaries are 

shown by dashed white lines, and white arrows indicate directions of vessel traffic. Two-way arrow marks the deep-water route 

for vessels of draft greater than 45 feet (13.7 m). Note that several of the bedrock knobs (red dots) are in the traffic lanes, and 

Harding Rock is even close to the deep-draft lane. Base map is composed of USGS shaded-relief images (see fig. 2).
22 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Figure 22. Large, modern oil tankers, when fully loaded, ride low in 

the water. However, as this combination photograph/diagram shows, 

the hull of the ship extends several 

tens of feet below the surface. 

(Image courtesy of Petroleum 

Association of Japan.)

Figure 21. A large container 

ship unloading cargo at the 

Port of Oakland. (Photograph 

courtesy of National Oceanographic and Atmospheric 

Administration.)
Areas and Issues of West-Central San Francisco Bay 23

is projected to increase to 14,000 by 2010 (Port of Oakland, 

Benefiting the California economy: unpub. data accessed 

online November 29, 2000, at http://www.portofoakland.com/

maritime/vision_07.html).

Tankers arriving at the Port of Richmond and the Port of 

Benicia together annually carry millions of gallons of crude 

oil that supplies refineries and ultimately consumers in the San 

Francisco Bay region. Although there have been no reported 

groundings of oil tankers on the bedrock knobs in the bay (Rogers, 1996), there have been other oil spills in San Francisco Bay 

that can be used to estimate the amount of potential damage that 

might be caused if a tanker struck one of these knobs. For example, an 8,000-gallon oil spill in October 1996 in San Francisco 

Bay cost approximately $10 million to clean up. A much larger 

spill at the Martinez oil refinery in San Pablo Bay (north San 

Francisco Bay) in 1988 cost $14 million to remediate. Annually, 

700 to 1,000 oil tankers of all sizes enter San Francisco Bay and 

transit through west-central bay on their way to anchorages and 

refineries and carry an average of 800 million barrels of oil per 

year (Nolte, 1997). Furthermore, deep-draft container vessels 

and other large vessels can carry thousands to tens of thousands 

of barrels of fuel oil, enough that any grounding on their part 

could create an environmental crisis.

Alcatraz Disposal Site

One of the most prominent features on the floor of 

west-central San Francisco Bay is a disposal site located just 

southwest of Alcatraz Island (figs. 20, 23). This disposal site, 

used for material dredged from shipping channels in the bay, 

is bounded by Alcatraz Island to the northeast and Alcatraz 

Shoal to the west. The disposal site covers an area of about 

0.25 square mile (0.64 km2), larger than the exposed landmass 

of Alcatraz Island (fig. 20). Water depths over the site in 1997 

ranged from 33 to 36 feet (10-11 m) at the shallowest to about 

65 to 82 feet (20-25 m) (fig. 20).

The first dredged waterway in San Francisco Bay was 

created in 1868; San Francisco Bay has been dredged periodically ever since. The increased waterborne commerce 

associated with and following the Gold Rush accelerated the 

requirement for dredging in San Francisco Bay to ensure navigable waterways. Dredging one part of the bay and disposing 

of the dredged material in another, open-water part of the bay 

(the Alcatraz site in particular), was the accepted method of 

operation for many decades. Dredged materials were disposed 

of at the Alcatraz site beginning in 1894, although it was not 

designated an official dredge disposal site until 1972 (U.S. 

Environmental Protection Agency, 1996).

Before 1894, the bay floor at the location of the Alcatraz 

Disposal Site was a topographic depression (fig. 23) with a 

maximum depth of about 165 feet (50 m) MLLW (U.S. Environmental Protection Agency, 1996). This topographic depression was probably similar to the present depression south and 

southeast of Point Blunt off Angel Island (fig. 20).

The Alcatraz Disposal Site was originally chosen because 

it was deep and it was assumed that the strong tidal currents that 

flow through west-central San Francisco Bay would disperse 

dredged material from the site. A study in 1987 demonstrated 

that there was no significant change in sediment composition 

at the Alcatraz Disposal Site for 1 to 3 months after disposal of 

material, suggesting that material remained at the site for at least 

that long (U.S. Environmental Protection Agency, 1996).

By 1982, the mound of material at the Alcatraz Disposal Site had become a potential navigational hazard, rising 

to within about 36 feet (11 m) of the water surface (Long 

Term Management Strategy, 1995). In 1987, USACE began 

requiring all disposal materials to be slurried or broken up 

and regulated the type, volume, and frequency of disposal, 

helping to limit further growth of the mound (Long Term 

Management Strategy, 1995). Since 1989, both yearly and 

monthly limits on dredge material disposal have been in 

effect for the Alcatraz site. However, continued mounding of 

dredged materials has generated increased concern about the 

fate, erodibility, and dispersion of the material dumped at the 

site (Long Term Management Strategy, 1995).

Using the 1997 multibeam dataset and GIS tools, the 

USGS made projections of the past and present volume 

and nature of sediment at the Alcatraz Disposal Site to aid 

in assessing the scope of the mounding problem (fig. 23). 

This projection showed that, as of spring 1997, there were 

approximately 8.7 million cubic yards (6.7 million m3

) of 

sediment in the mound at the disposal site.

Dredging Issues

Two general types of dredging occur within west-central 

and adjacent parts of San Francisco Bay—(1) sand mining for 

construction aggregate and (2) maintenance and improvement 

dredging of harbors and navigation waterways. Maintenance 

dredging alleviates short-term problems, such as shoaling of 

harbors, waterways, or channels, but carries with it the problem of dredge material disposal. Dredging, no matter for what 

purpose, alters the environment of the bay floor. If the dredged 

area does not refill with native material of the same grain size 

and composition, the change can be permanent. If the bay 

floor does not fill back in or refills with different material, the 

biological habitat at the dredge site will be altered.

Sand Mining in West-Central Bay

Millions of cubic yards of sand and gravel have been 

permanently removed from bay-floor shoals since 1915. The 

process continues today, as active sand-mining leases allow 

private contractors to extract sand and gravel from submerged 

State lands on a permit basis (fig. 14). At present no fewer 

than 10 sand-mining lease sites exist in west-central San 

Francisco Bay that are regulated by the California State Lands 

Commission (CSLC).

Sidescan-sonar and multibeam surveys of Point Knox 

Shoal in west-central bay in 1975 (Rubin and McCulloch, 

1979) and 1997 (Chin and others, 1998) both show bay-floor 
24 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Figure 23. Evolution of the bay floor in the 

area of the Alcatraz Disposal Site. Oblique 

images show the topography of the bottom 

in 1894, during the period 1960-80, and in 

1997. The 1997 image is derived from 1997 

U.S. Geological Survey multibeam survey 

(95 kHz) of west-central San Francisco Bay. 

Images for earlier times constructed from 

available data. Cross section shows how 

dumping of dredged material in the Alcatraz 

Disposal Site transformed a bay-floor 

depression into a mound reaching within 

33 feet (10 m) of the water surface. Modified 

from Chin and others (1998).

Outline of 

Alcatraz Disposal Site

Reconstruction of 

1894 bay floor showing 

maximum depth of 

165 feet (50 meters)

1894

Alcatraz Island

Outline of 

Alcatraz Disposal Site

Reconstruction of 

1960-80 (?) bay floor at an 

intermediate filling level

Alcatraz Island

1960–80

Image derived from 

1997 survey, showing 

current fill level

Alcatraz Island

N

Outline of 

Alcatraz Disposal Site

1997

Reference mesh of

100-yd (91 m) squares

Vertical exaggeration:

Water: 10x

Land: 2x

EXPLANATION

Disposal Site

0 500 1000 1500 2000 2500 3000 3500

DISTANCE, IN FEET

EXPLANATION

-150

-100

-50

0

50

100

ELEVATION, IN FEET

0 200 400 800 1000

DISTANCE, IN METERS

-50

-40

-30

-20

-10

0

10

20

30

ELEVATION, IN METER

N S

VERTICAL EXAGGERATION = 5X

600

1997 5,407,000 cubic yards

(4,134,000 m3)

1960-80(?)

1894

Estimated total volume within

disposal site in 1997: 8.8

million cubic yards (6.7

million cubic meters)

3,387,000 cubic yards

(2,589,000 m3)

Alcatraz

Island
Areas and Issues of West-Central San Francisco Bay 25

features attributable to sand mining. The physical alteration 

of the bay floor on Point Knox Shoal, as shown by the 1997 

USGS multibeam survey (fig. 2), is significant. The dredgerelated features are so numerous as to literally obliterate the 

fabric of the bay floor (fig. 16). More recent dredging has 

further modified the bay floor on the shoal (fig. 15). It is not 

known how long the topographic depressions interpreted as 

dredge-related persist on the bay floor. It is also not known 

whether and how these depressions fill in after dredging.

The total volume of sand in the west-central bay shoals that 

are in active sand mining leases is unknown. Sand miners conduct 

yearly hydrographic surveys of their lease sites in the bay as 

required by permitting agencies. However, changes indicated by 

these surveys do not reveal what is happening in three dimensions 

on the shoals or their adjacent areas, nor do they yield an accurate 

inventory of sand resources. The volume of commercially extractable sand and gravel in these shoals needs to be known to prevent 

resource depletion. Additionally, it is not known whether the sand 

shoals in west-central bay are being naturally replenished, are in 

equilibrium, or are eroding. Natural sand replenishment could 

come from material flowing through the Sacramento-San Joaquin 

Delta and the north bay, from local sources such as eroding bedrock, or from sediment carried in from beyond the Golden Gate.

Maintenance and Improvement Dredging

Any discussion of maintenance and improvement dredging 

in west-central San Francisco Bay should be seen in a national 

and regional dredging perspective. The United States annually 

spends about $800 million to dredge more than 400 million 

cubic yards (300 million m3) of sediment from ports, harbors, 

and waterways (Patella, 2000). This amount of dredged material 

would cover a four-lane highway stretching from Los Angeles 

to New York City to a depth of 4 feet (1.2 m), or fill one million 

dump trucks (American Association of Port Authorities, Port 

Facts and Statistics: unpub. data accessed online November 29, 

2000 at http://www.aapa-ports.org/portedu.html). The present and future trend for shipping in U.S. ports is for fewer but 

larger vessels. The draft of these larger vessels is critical to their 

economy of scale but affects each port’s ability to accommodate 

them. A loss of 1 inch (2.5 cm) in draft for a vessel of 1,000-

foot (305 m) length can result in the loss of as much as 270 tons 

of cargo-carrying capacity (Patella, 2000).

Maintenance and improvement dredging has become increasingly important since the first Federal navigation channel was 

created in the 1800’s. However, the dredging process has also come 

under greater scrutiny because of environmental concerns. For 

example, nationally, 3 to 5 percent of dredged material is contaminated and cannot be reused for beneficial purposes (Patella, 2000).

About 6 million cubic yards (4.6 million m3

) of sediment 

is dredged from San Francisco Bay each year (Goldbeck, 

1999). This volume includes only maintenance dredging of 

existing waterways, not new projects, and volumes typically 

vary from year to year. The San Francisco Bar Channel, just 

outside the Golden Gate, is dredged to a maintenance depth of 

56 feet (17 m) MLLW. The deep passage through the Golden 

Gate itself is approximately 330 feet (101 m) MLLW and 

is naturally scoured by tidal currents. The tops of Harding, 

Shag, Arch, and Blossom Rocks in west-central bay are all 

in the range of 36 to 40 feet (11-12 m) MLLW. The Alcatraz 

Disposal Site’s shoal depth varies, but the USGS multibeam 

survey in the spring of 1997 showed it to be 33 to 36 feet 

(10-11 m) MLLW. Water depth under other parts of the deepwater vessel-traffic lanes is about 53 feet (16 m) MLLW at 

the shallowest. Within 0.3 mile (0.5 km) northeast of Alcatraz 

Island the water depth shoals to about 40 to 46 feet (12-14 

m) MLLW, although this area is not in the deep-water vessel 

traffic lane.

In the San Francisco Bay area, dredging and the disposal 

of dredged material are managed by a consortium of agencies, which have established the Long Term Management 

Strategy (LTMS) program. This group consists of the San 

Francisco Bay Conservation and Development Commission 

(BCDC), San Francisco Bay Regional Water Quality Control Board (RWQCB), State Water Resources Control Board 

(WRCB), U.S. Environmental Protection Agency (USEPA), 

and USACE. Local entities that have an interest in dredging 

and disposal also participate in the LTMS. The LTMS was 

established in 1991 to resolve controversies regarding dredged 

material disposal.

Before 1991, most dredged material from San Francisco 

Bay projects had been disposed of at the Alcatraz Disposal 

Site and other in-bay sites. However, by the mid-1980’s, the 

Alcatraz mound had grown to the extent that it had become a 

navigational hazard, indicating that dredged material dumped 

there was not dispersing. Fishermen and environmentalists 

protested that the mud dumped at Alcatraz was harmful to 

marine life, and they blockaded the dumpsite in 1989 (Goldbeck, 1999). Years of “mudlock” resulted, when dredged 

material lacked a local site for disposal, and maintenance and 

improvement dredging had to be diminished until a solution 

was found. The disposal of dredged material is not a modern problem. As early as the late 1800’s, USACE showed 

concern over the effects of the disposal of dredged material 

in San Francisco Bay (Hagwood, 1982).

The LTMS has alleviated “mudlock” in San Francisco Bay by getting all interested parties to work together 

for solutions. Using the results of USGS studies, USEPA 

designated the San Francisco Deep-Ocean Disposal Site 

(SFDODS) in 1994, 55 miles (88 km) outside the Golden 

Gate in the Pacific Ocean in water depths of 8,200 to 9,800 

feet (2,500-3,000 m) (Karl and others, 2001). LTMS has 

coordinated and streamlined the processing of permit applications for dredging and dredged-material disposal. LTMS 

has the mission of coordinating dredging and disposal for the 

San Francisco Bay area for 50 years from 1991.

The LTMS strategy will use as much dredged material as possible for wetland restoration and other beneficial 

reuse projects, but about 20 percent of dredged material will 

continue to be disposed of at sites in the bay, and the remainder will be taken to SFDODS. This strategy will be phased 

in over a decade (Goldbeck, 1999). The long-term success of 
26 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

Figure 24. Vast changes have occurred to the wetlands around the San Francisco Bay and Delta estuary as a result of development and population increase. The maps show the distribution of various types of wetlands around 1800, before any significant 
Areas and Issues of West-Central San Francisco Bay 27

development (names on map are Native American tribal regions), and what had happened to those areas by 1998. Modified from 

Bay Area EcoAtlas (1999). Shaded relief by Graham and Pike (1997).
28 Shifting Shoals and Shattered Rocks—How Man Has Transformed the Floor of West-Central San Francisco Bay

the LTMS in San Francisco Bay appears largely dependent on 

the availability of local wetland restoration sites for beneficial 

reuse of dredged material and on the political will to continue 

with restoration, even at higher costs than for in-bay disposal.

Wetland restoration is at present an important process in 

the San Francisco Bay estuary, where more than 90 percent 

of the natural wetlands have been lost to man’s activities 

since the 1800’s (fig. 24). Large areas of baylands were diked 

off, drained, and used for agriculture. These diked areas 

have subsided, in many cases below the low tide elevation, 

and restoring them as tidal wetlands requires filling with 

sediment to raise them back to within the tidal range. San 

Francisco Bay benefits from having tidal wetland restoration 

sites located relatively close to ports where sediment needs 

to be dredged. There is an abundance of diked baylands that 

are well suited and politically acceptable for wetland restoration (Estuary, 1996). Many of those targeted for restoration 

will use dredged material beneficially. However, the cost of 

wetland restoration can be very great, ranging from $20,000 

to as much as $80,000 per acre (Ernest and others, 1995).

The Port of Oakland completed its “42 ft Harbor Deepening Project” (13 m MLLW) in 1998 (Howton, 1999). A 

significant quantity of the dredged sediment from that major 

project was used at the Sonoma baylands wetland restoration 

site in San Pablo Bay (north San Francisco Bay). The port 

estimated that the cost to transport dredged material the additional distance to Sonoma baylands, rather than locally to the 

nearby Alcatraz Disposal Site, increased their disposal costs 

by less than 5 percent (Ernest and others, 1995). Disposal of 

dredged material at the wetland restoration site cost $10 per 

cubic yard, disposal at SFDODS cost $8 per cubic yard, and 

onland disposal of mildly contaminated mud at a local golf 

course cost $22 per cubic yard (Estuary, 1996).

The Port of Oakland has been in the process of dredging its harbor entrance and docking facilities to a depth of 50 

feet (15 m) MLLW (“50 ft Harbor Deepening Project”). The 

deepening of the port entrance to 50 feet (15 m) is predicated 

on the port’s desire to accommodate the latest generation 

of deep-draft, high-capacity container vessels. These newer 

vessels carry more units of cargo at lower cost per unit, 

producing economies of scale (Port of Oakland, Vision 2000: 

unpub. data accessed online November 29, 2000, at http:

//www.portofoakland.com/maritime/vision_02.html). The 

deep-draft container vessels, which draw 50 feet (15 m) fully 

loaded, are expected within several years to make up more 

than 75 percent of the world’s container ship capacity.

The Port of Richmond recently completed deepening 

its harbor to 40 feet (12 m) MLLW. The largest oil tankers 

calling at the port already draw almost 40 feet of water. The 

Port of San Francisco has harbor facilities that are as deep as 

43 feet (13 m) MLLW. Its facilities are mainly used for other 

non-cargo purposes, such as the berthing of tugboats, cruise 

ships, and passenger ferries (San Francisco Bay Conservation and Development Commission and Oakland Metropolitan Transportation Commission, 1996).

Conclusion

San Francisco Bay is one of the world’s most beautiful natural harbors and a magnet both for maritime trade 

and for millions of visitors. Two hundred years ago, the 

natural environment of the bay had hardly been affected 

by the presence of local communities of Native Americans 

and very small numbers of Europeans. All that changed 

with the discovery of gold in California in the middle of 

the 19th century. San Francisco became the gateway for 

ships bearing miners, settlers, and commercial trade. The 

population of the bay region burgeoned, and great cities, 

ports, bridges, and other engineering works were built. The 

bay area’s population and associated development have 

increasingly changed the estuary and its environment. The 

bay became a resource for dredged material to provide 

fill, and also a place to dispose of material excavated from 

waterways. Much of this activity was in the central part of 

the bay, where the major shipping lanes diverge after passing through the Golden Gate. To provide adequate water 

depth for the increasing draft of ships, emergent or shallow 

bedrock knobs were repeatedly blasted. By the late 20th 

century, San Francisco Bay had become a heavily urbanized 

estuary perhaps more modified by man’s activities than any 

other major estuary in the United States.

The floor of San Francisco Bay is hidden beneath its 

scenic surface, and the changes man has made there since the 

Gold Rush are not readily visible. However, studies by the 

U.S. Geological Survey and others have revealed details of 

the transformed floor of the bay—depressions and grooves 

on shoals excavated by dredging, shallow areas created by 

irregular piles of disposed material, and shattered rocks on 

the truncated tops of bedrock knobs. The bay continues to be 

affected by human activities, interacting dynamically with 

the natural physical, chemical, and biological processes that 

constantly mold its environment, and the future surely will 

see more modifications. Scientific studies of these varied 

processes and activities and their likely consequences will 

help provide the understanding on which wise planning decisions can be based. Providing safe navigation channels for 

commercial vessels of ever-deeper drafts while also protecting the biological habitats in the bay will provide critical and 

complex challenges for the future.

Acknowledgments

A number of individuals contributed to this paper. We 

would especially like to thank Dave Cacchione, Dave Rubin, 

Pat Chavez, Bruce Rogers, Jim Gardner, Pete Dartnell, Hank 

Chezar of the USGS, the USGS Marine Facility, Capt. Thomas 

Richards (NOAA), Art Kleiner (C&C Technologies), and 

Capt. Gordon Smith (University of California, Santa Cruz). 

We also thank Steve Goldbeck (BCDC) and Steve Eittreim 

(USGS) for their constructive reviews.
References 29

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