California State Waters Map Series—Offshore of Tomales 

Point, California

By Samuel Y. Johnson, Peter Dartnell, Nadine E. Golden, Stephen R. Hartwell, H. Gary Greene, Mercedes D. 

Erdey, Guy R. Cochrane, Janet T. Watt, Rikk G. Kvitek, Michael W. Manson, Charles A. Endris, Bryan E. Dieter, 

Lisa M. Krigsman, Ray W. Sliter, Erik N. Lowe, and John L. Chin

(Samuel Y. Johnson and Susan A. Cochran, editors)

Pamphlet to accompany 

Open-File Report 2015–1088

2015

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2015

For more information on the USGS—the Federal source for science about the Earth,

its natural and living resources, natural hazards, and the environment—visit 

http://www.usgs.gov/ or call 1–888–ASK–USGS (1–888–275–8747).

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

visit http://www.usgs.gov/pubprod/. 

To order this and other USGS information products, visit http://store.usgs.gov/. 

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

endorsement by the U.S. Government.

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

contain copyrighted materials as noted in the text. Permission to reproduce copyrighted items

must be secured from the copyright owner.

Suggested citation:

Johnson, S.Y., Dartnell, P., Golden, N.E., Hartwell, S.R., Greene, H.G., Erdey, M.D., Cochrane, G.R., Watt, J.T., 

Kvitek, R.G., Manson, M.W., Endris, C.A., Dieter, B.E., Krigsman, L.M., Sliter, R.W., Lowe, E.N., and Chin, J.L.

(S.Y. Johnson and S.A. Cochran, eds.), 2015, California State Waters Map Series—Offshore of Tomales Point, 

California: U.S. Geological Survey Open-File Report 2015–1088, pamphlet 38 p., 10 sheets, scale 1:24,000, 

http://dx.doi.org/10.3133/ofr20151088. 

ISSN 2331-1258 (online)
iii

Contents

Preface...........................................................................................................................................................................1

Chapter 1. Introduction...................................................................................................................................................3

By Samuel Y. Johnson

Publication Summary..................................................................................................................................................5

Chapter 2. Bathymetry and Backscatter-Intensity Maps of the Offshore of Tomales Point Map Area (Sheets 1, 2, 

and 3).............................................................................................................................................................................8

By Peter Dartnell and Rikk G. Kvitek

Chapter 3. Data Integration and Visualization for the Offshore of Tomales Point Map Area (Sheet 4) ........................10

By Peter Dartnell

Chapter 4. Seafloor-Character Map of the Offshore of Tomales Point Map Area (Sheet 5).........................................11

By Mercedes D. Erdey and Guy R. Cochrane

Chapter 5. Ground-Truth Studies for the Offshore of Tomales Point Map Area (Sheet 6) ...........................................16

By Nadine E. Golden and Guy R. Cochrane

Chapter 6. Potential Marine Benthic Habitats of the Offshore of Tomales Point Map Area (Sheet 7)..........................19

By H. Gary Greene, Charles A. Endris, and Bryan E. Dieter

Classifying Potential Marine Benthic Habitats ..........................................................................................................19

Examples of Attribute Coding ...................................................................................................................................21

Map Area Habitats....................................................................................................................................................21

Chapter 7. Subsurface Geology and Structure of the Offshore of Tomales Point Map Area and the Salt Point to 

Drakes Bay Region (Sheets 8 and 9)...........................................................................................................................22

By Samuel Y. Johnson, Stephen R. Hartwell, Janet T. Watt, Ray W. Sliter, and John L. Chin

Data Acquisition........................................................................................................................................................22

Seismic-Reflection Imaging of the Continental Shelf................................................................................................23

Geologic Structure and Recent Deformation ............................................................................................................23

Thickness and Depth to Base of Uppermost Pleistocene and Holocene Deposits ...................................................24

Chapter 8. Geologic and Geomorphic Map of the Offshore of Tomales Point Map Area (Sheet 10)............................27

By Samuel Y. Johnson, Michael W. Manson, Stephen R. Hartwell, and H. Gary Greene

Geologic and Geomorphic Summary........................................................................................................................27

Description of Map Units ..........................................................................................................................................30

Offshore Geologic And Geomorphic Units ............................................................................................................30

Onshore Geologic And Geomorphic Units ............................................................................................................31

Acknowledgments........................................................................................................................................................33

References Cited .........................................................................................................................................................34

Figures

Figure 1–1. Physiography of northern California coast from Point Arena to San Francisco........................................... 6

Figure 1–2. Coastal geography of Offshore of Tomales Point map area....................................................................... 7

Figure 4–1. Detailed view of ground-truth data, showing accuracy-assessment methodology.................................... 13

Figure 5–1. Photograph of camera sled used in USGS 2008 ground-truth survey ...................................................... 16

Figure 5–2. Graph showing distribution of primary and secondary substrate determined from video observations in 

Offshore of Tomales Point map area........................................................................................................ 18
iv

Tables

Table 4–1. Conversion table showing how video observations of primary substrate, secondary substrate, and 

abiotic seafloor complexity are grouped into seafloor-character-map Classes I, II, and III for use in 

supervised classification and accuracy assessment in Offshore of Tomales Point map area................... 14

Table 4–2. Accuracy-assessment statistics for seafloor-character-map classifications in Offshore of Tomales Point 

map area .................................................................................................................................................. 15

Table 7–1. Area, sediment-thickness, and sediment-volume data for California’s State Waters in Salt Point to 

Drakes Bay region, as well as in Offshore of Tomales Point map area .................................................... 26

Table 8–1. Areas and relative proportions of offshore geologic map units in Offshore of Tomales Point map area... 29

Map Sheets

Sheet 1. Colored Shaded-Relief Bathymetry, Offshore of Tomales Point Map Area, California

By Peter Dartnell and Rikk G. Kvitek 

Sheet 2. Shaded-Relief Bathymetry, Offshore of Tomales Point Map Area, California 

By Peter Dartnell and Rikk G. Kvitek

Sheet 3. Acoustic Backscatter, Offshore of Tomales Point Map Area, California 

By Peter Dartnell, Mercedes D. Erdey, and Rikk G. Kvitek 

Sheet 4. Data Integration and Visualization, Offshore of Tomales Point Map Area, California 

By Peter Dartnell 

Sheet 5. Seafloor Character, Offshore of Tomales Point Map Area, California 

By Mercedes D. Erdey and Guy R. Cochrane 

Sheet 6. Ground-Truth Studies, Offshore of Tomales Point Map Area, California 

By Nadine E. Golden, Guy R. Cochrane, and Lisa M. Krigsman 

Sheet 7. Potential Marine Benthic Habitats, Offshore of Tomales Point Map Area, California 

By Charles A. Endris, H. Gary Greene, Bryan E. Dieter, Erik N. Lowe, and Mercedes D. Erdey 

Sheet 8. Seismic-Reflection Profiles, Offshore of Tomales Point Map Area, California 

By Samuel Y. Johnson, Ray W. Sliter, Stephen R. Hartwell, and John L. Chin 

Sheet 9. Local (Offshore of Tomales Point Map Area) and Regional (Offshore from Salt Point to Drakes Bay) 

Shallow-Subsurface Geology and Structure, California 

By Samuel Y. Johnson, Stephen R. Hartwell, Janet T. Watt, and Ray W. Sliter 

Sheet 10. Offshore and Onshore Geology and Geomorphology, Offshore of Tomales Point Map Area, California 

By Stephen R. Hartwell, Samuel Y. Johnson, and Michael W. Manson
1

California State Waters Map Series—Offshore of Tomales 

Point, California

By Samuel Y. Johnson,1 Peter Dartnell,1 Nadine E. Golden,1 Stephen R. Hartwell,1 H. Gary Greene,2 Mercedes D. 

Erdey,1 Guy R. Cochrane,1 Janet T. Watt,1 Rikk G. Kvitek,3 Michael W. Manson,4 Charles A. Endris,2 Bryan E. 

Dieter,2 Lisa M. Krigsman,5 Ray W. Sliter,1 Erik N. Lowe,1 and John L. Chin1

(Samuel Y. Johnson1 and Susan A. Cochran,1 editors)

Preface 

In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping 

Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, 

marine benthic habitats, and geology within California’s State Waters. The program supports a large 

number of coastal-zone- and ocean-management issues, including the California Marine Life Protection 

Act (MLPA) (California Department of Fish and Wildlife, 2008), which requires information about the 

distribution of ecosystems as part of the design and proposal process for the establishment of Marine 

Protected Areas. A focus of CSMP is to map California’s State Waters with consistent methods at a 

consistent scale.

The CSMP approach is to create highly detailed seafloor maps through collection, integration, 

interpretation, and visualization of swath sonar data (the undersea equivalent of satellite remote-sensing 

data in terrestrial mapping), acoustic backscatter, seafloor video, seafloor photography, high-resolution 

seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor 

morphology and character, identify potential marine benthic habitats, and illustrate both the surficial 

seafloor geology and shallow (to about 100 m) subsurface geology. It is emphasized that the more 

interpretive habitat and geology maps rely on the integration of multiple, new high-resolution datasets 

and that mapping at small scales would not be possible without such data. 

This approach and CSMP planning is based in part on recommendations of the Marine Mapping 

Planning Workshop (Kvitek and others, 2006), attended by coastal and marine managers and scientists 

from around the state. That workshop established geographic priorities for a coastal mapping project and 

identified the need for coverage of “lands” from the shore strand line (defined as Mean Higher High 

Water; MHHW) out to the 3-nautical-mile (5.6-km) limit of California’s State Waters. Unfortunately, 

surveying the zone from MHHW out to 10-m water depth is not consistently possible using ship-based 

surveying methods, owing to sea state (for example, waves, wind, or currents), kelp coverage, and 

shallow rock outcrops. Accordingly, some of the maps presented in this series commonly do not cover 

the zone from the shore out to 10-m depth; these “no data” zones appear pale gray on most maps. 

 

1 U.S. Geological Survey

2 Moss Landing Marine Laboratories, Center for Habitat Studies

3 California State University Monterey Bay, Seafloor Mapping Lab

4 California Geological Survey

5 National Oceanic and Atmospheric Administration, National Marine Fisheries Service
2

This map is part of a series of online U.S. Geological Survey (USGS) publications, each of 

which includes several map sheets, some explanatory text, and a descriptive pamphlet. Each map sheet 

is published as a PDF file. Geographic information system (GIS) files that contain both ESRI6 ArcGIS 

raster grids (for example, bathymetry, seafloor character) and geotiffs (for example, shaded relief) are 

also included for each publication. For those who do not own the full suite of ESRI GIS and mapping 

software, the data can be read using ESRI ArcReader, a free viewer that is available at 

http://www.esri.com/software/arcgis/arcreader/index.html (last accessed March 10, 2014).

The California Seafloor Mapping Program (CSMP) is a collaborative venture between numerous 

different federal and state agencies, academia, and the private sector. CSMP partners include the 

California Coastal Conservancy, the California Ocean Protection Council, the California Department of 

Fish and Wildlife, the California Geological Survey, California State University at Monterey Bay’s 

Seafloor Mapping Lab, Moss Landing Marine Laboratories Center for Habitat Studies, Fugro Pelagos, 

Pacific Gas and Electric Company, National Oceanic and Atmospheric Administration (NOAA, 

including National Ocean Service—Office of Coast Surveys, National Marine Sanctuaries, and National 

Marine Fisheries Service), U.S. Army Corps of Engineers, the Bureau of Ocean Energy Management, 

the National Park Service, and the U.S. Geological Survey. 

 

6 Environmental Systems Research Institute, Inc.
3

Chapter 1. Introduction

By Samuel Y. Johnson

The map area offshore of Tomales Point, California, which is referred to herein as the “Offshore 

of Tomales Point” map area (figs. 1–1, 1–2), is located in northern California, about 60 km north of San 

Francisco and 110 km south of Point Arena. The map area includes offshore waters, Tomales Point (the 

north end of the Point Reyes Peninsula), the northern part of Tomales Bay, and coastal lands east of 

Tomales Bay (fig. 1–2). The onshore part of the map area is largely undeveloped, used primarily for 

recreation and ranching, as well as oyster farming in Tomales Bay. The Point Reyes Peninsula is part of 

the Point Reyes National Seashore, and two small areas on the east coast of Tomales Bay are part of the 

Golden Gate National Recreation Area. The small towns of Tomales and Dillon Beach (populations 204 

and 283, respectively, 2010 census) are the largest cultural centers. 

Tomales Bay (fig. 1–2), approximately 20-km long and 1- to 2-km wide, formed along a 

submerged portion of the San Andreas Fault (fig. 1–2), which forms a right-lateral transform boundary 

between the North American and Pacific tectonic plates. The fault juxtaposes Cretaceous granitic rock to

the southwest (exposed on Tomales Point) with the Jurassic and Cretaceous Franciscan Complex to the 

northeast (exposed on the northeast coast of the Tomales Bay), and has an estimated slip rate of about 17 

to 30 mm/yr in this area (Bryant and Lundberg, 2002; Grove and Niemi, 2005). The destructive great 

1906 California earthquake (M7.8, 4/18/1906) is thought to have nucleated on the San Andreas Fault 

about 60 km to the south, offshore of San Francisco (for example, Bolt, 1968; Lomax, 2005), with the 

rupture extending northward through Tomales Bay and for an additional about 230 km to the south flank 

of Cape Mendocino. 

The northwest coast of Tomales Point is characterized by steep, high (as much as 100 m), barren, 

granitic cliffs and a rugged shoreline with a few small pocket beaches. Hapke and Reid (2007) 

documented that as much as 48 m of Tomales Point cliff retreat occurred from 1929–30 to 2002, at rates 

ranging from about 0.1 to 0.85 m/yr. The granite is in contact with less resistant Tertiary sandstones at 

Kehoe Beach (fig. 1–2), the northern end of a continuous, wide, sandy beach backed by a large coastal 

dune field that extends for about 20 km south to Point Reyes Head (fig. 1–1). Hapke and others (2006) 

indicate that the central about 13 km of the Point Reyes Beach has a long-term (from the middle to late 

1800s to 2001) history of accretion, at rates of 0.1 to 1.0 m/yr. Over the short term (1952 to 2001), this 

beach has a mixed history of accretion and retreat, at rates ranging from -0.7 to 2.0 m/yr (negative 

numbers indicate beach erosion, positive numbers indicate beach accretion). Both the northern about 2 

km and the southern about 5 km of this long beach have mixed to erosional shoreline-change histories. 

Long-term and short-term change rates in the northern part of the beach range from 0.2 to 0.3 m/yr and -

0.1 to -0.9 m/yr, respectively. Long-term and short-term change rates in the southern about 5 km of this 

long beach range from -0.5 to 0.3 m/yr and -0.1 to -3.0 m/yr, respectively. 

Tomales Point relief is asymmetrical so that most small coastal watersheds in the map area drain 

eastward from Inverness Ridge into Tomales Bay. Many of these steep drainages have small sandy 

beaches at their mouths. The east coast of Tomales Bay is characterized by more gentle, hummocky, 

hilly relief underlain by the landslide-prone Franciscan Complex. Keys Creek, the most prominent small 

watershed entering Tomales Bay from the east, has a small subaqueous delta at its mouth. 

Sand Point and Dillon Beach are located at the mouth of Tomales Bay and on the 

southeasternmost shores of Bodega Bay, respectively (fig. 1–2). The wide beach in this area is backed 

by an extensive (4.8 km2

) sand-dune complex. The enormous volume of sand on the beach and in the 

dune field is derived from southward littoral drift. This sediment is trapped by Tomales Bay and 
4

Tomales Point, which function as the south end of the Bodega Bay littoral cell (Habel and Armstrong, 

1978). Hapke and others (2006) indicate that Dillon Beach has been accreting at rates of 0.1 to 1.8 m/yr 

over the long term (since the mid to late 1800s) and rates of 0.2 to 2.7 m/yr over the short term (1952 to 

2002). 

Based on high-resolution bathymetry, sediment sampling, and foraminiferal analyses, Anima and 

others (2008) divided Tomales Bay into three distinct areas. The Offshore of Tomales Point map area 

includes all of their Area A at the mouth of Tomales Bay, and the northern part of their Area B in the 

central bay. Area A is characterized by sand waves, dunes, and flats formed in response to strong tidal 

flow. In contrast, Area B to the southeast is generally flat and underlain by finer grained sand and silt. 

The continental shelf in California’s State Waters in the Offshore of Tomales Point map area 

extends to water depths of about 70 m (mean slope of about 0.7°) and is characterized by extensive, 

rugged, rocky seafloor. Granitic seafloor has a massive and fractured texture, whereas seafloor 

sedimentary rock outcrops commonly form distinctive “ribs” created by differential seafloor erosion of 

dipping beds of variable resistance. Direct sediment supply to this shelf is minimal because littoral drift 

is blocked to the north by Tomales Bay and Tomales Point, and to the south by the Point Reyes 

headland. 

Potential marine benthic habitats in the Offshore of Tomales Point map area range from 

unconsolidated continental-shelf sediment, to rocky continental-shelf substrate, to unconsolidated 

estuary sediments. Rocky-shelf outcrops and rubble are considered to be promising potential habitats for 

rockfish and lingcod (Cass and others, 1990; Love and others, 2002), both of which are recreationally 

and commercially important species. Dynamic bedforms, such as the sand waves at the mouth of 

Tomales Bay, are considered potential foraging habitat for juvenile lingcod and possibly migratory 

fishes (Beaudreau, 2005), as well as for forage fish such as Pacific sand lance. 

Circulation over the continental shelf in the map area (and in the broader northern California 

region) is dominated by the southward-flowing California Current, the eastern limb of the North Pacific 

Gyre (Hickey, 1979). Associated upwelling brings cool, nutrient-rich waters to the surface, resulting in 

high biological productivity. The current flow generally is southeastward during the spring and summer; 

however, during the fall and winter, the otherwise persistent northwest winds are sometimes weak or 

absent, causing the California Current to move farther offshore and the Davidson Current, a weaker, 

northward-flowing countercurrent (Hickey, 1979), to become active. As a result, net flow over the 

continental shelf can be more southerly during the spring and summer and more northerly during the fall 

and winter. 

Throughout the year, this part of the central California coast is exposed to four wave climate 

regimes—the north Pacific swell, the southern swell, northwest wind waves, and local wind waves 

(Storlazzi and Griggs, 2000; Storlazzi and Wingfield, 2005). The north Pacific swell dominates in winter 

months (typically November through March), with wave heights at offshore buoys ranging from 2 to 10 

m and wave periods ranging from 10 to 25 s (Storlazzi and Wingfield, 2005). During summer months, 

the largest waves come from the southern swell, generated by storms in the south Pacific and offshore 

Central America. Characteristically, these swells have smaller wave heights (0.3 to 3 m) and similarly 

long periods (range 10 to 25 s). Northwest wind waves affect the coast throughout the year, while local 

wind waves are most common from October to April. These two wind-wave regimes typically have 

wave heights of 1 to 4 m and short periods (3 to 10 s). 
5

Publication Summary

This publication about the Offshore of Tomales Point map area includes ten map sheets that 

contain explanatory text, in addition to this descriptive pamphlet, and a data catalog of geographic 

information system (GIS) files. Sheets 1, 2, and 3 combine data from four different sonar surveys to 

generate comprehensive high-resolution bathymetry and acoustic-backscatter coverage of the map area. 

These data reveal a range of physiographic features (highlighted in the perspective views on sheet 4) 

such as the prominent, massive to ribbed outcrops of granitic and sedimentary rocks, and flat, sedimentcovered seafloor offshore of Tomales Point and in Tomales Bay. To validate geological and biological 

interpretations of the sonar data shown in sheets 1, 2, and 3, the U.S. Geological Survey towed a camera 

sled over specific offshore locations, collecting both video and photographic imagery; this “groundtruth” surveying data is summarized on sheet 6. Sheet 5 is a “seafloor character” map, which classifies 

the seafloor on the basis of depth, slope, rugosity (ruggedness), and backscatter intensity and which is 

further informed by the ground-truth-survey imagery. Sheet 7 is a map of “potential habitats,” which are 

delineated on the basis of substrate type, geomorphology, seafloor process, or other attributes that may 

provide a habitat for a specific species or assemblage of organisms. Sheet 8 compiles representative 

seismic-reflection profiles from the map area, providing information on the subsurface stratigraphy and 

structure of the map area. Sheet 9 shows the distribution and thickness of young sediment (deposited 

over the last about 21,000 years, during the most recent sea-level rise), in both the map area and the 

larger offshore Salt Point to Drakes Bay region, interpreted on the basis of the seismic-reflection data, 

and it identifies the Offshore of Tomales Point map area as lying within in the Bodega-Tomales shelf 

domain. Sheet 10 is a geologic map that merges onshore geologic mapping (compiled from existing 

maps by the California Geological Survey) and new offshore geologic mapping that is based on 

integration of high-resolution bathymetry and backscatter imagery (sheets 1, 2, 3), seafloor-sediment 

and rock samples (Reid and others, 2006), digital camera and video imagery (sheet 6), high-resolution 

seismic-reflection profiles (sheet 8), and air-photo interpretation of the nearshore. 

The information provided by the map sheets, pamphlet, and data catalog have a broad range of 

applications. High-resolution bathymetry, acoustic backscatter, ground-truth-surveying imagery, and 

habitat mapping all contribute to habitat characterization and ecosystem-based management by 

providing essential data for delineation of marine protected areas and ecosystem restoration. Many of 

the maps provide high-resolution baselines that will be critical for monitoring environmental change 

associated with climate change, coastal development, or other forcings. High-resolution bathymetry is a 

critical component for modeling coastal flooding caused by storms and tsunamis, as well as inundation 

associated with longer term sea-level rise. Seismic-reflection and bathymetric data help characterize 

earthquake and tsunami sources, critical for natural-hazard assessments of coastal zones. Information on 

sediment distribution and thickness is essential to the understanding of local and regional sediment 

transport, as well as the development of regional sediment-management plans. In addition, siting of any 

new offshore infrastructure (for example, pipelines, cables, or renewable-energy facilities) will depend 

on high-resolution mapping. Finally, this mapping will both stimulate and enable new scientific research 

and also raise public awareness of, and education about, coastal environments and issues. 
6

Figure 1–1. Physiography of northern California coast from Point Arena to San Francisco (SF). Red box shows 

Offshore of Tomales Point map area. Yellow line shows limit of California’s State Waters. Other abbreviations: 

IR, Inverness Ridge; PRH, Point Reyes headland; SAFZ, San Andreas Fault Zone; TP, Tomales Point.
7

Figure 1–2. Coastal geography of Offshore of Tomales Point map area. Yellow line shows limit of California’s State 

Waters. Abbreviations: AL, Abbots Lagoon; BB, southernmost Bodega Bay; DB, Dillon Beach; IR, Inverness 

Ridge; KB, Kehoe Beach; KC, Keys Creek; SP, Sand Point; T, Tomales; To, Toms Point; TP, Tomales Point. 
8

Chapter 2. Bathymetry and Backscatter-Intensity Maps of the Offshore 

of Tomales Point Map Area (Sheets 1, 2, and 3)

By Peter Dartnell and Rikk G. Kvitek

The colored shaded-relief bathymetry (sheet 1), the shaded-relief bathymetry (sheet 2), and the 

acoustic-backscatter (sheet 3) maps of the Offshore of Tomales Point map area in northern California 

were generated from bathymetry and backscatter data collected by Fugro Pelagos, by California State 

University, Monterey Bay (CSUMB), and by the U.S. Geological Survey (USGS). Mapping was 

completed between 2004 and 2010, using a combination of 200-kHz and 400-kHz Reson 7125 and 244-

kHz Reson 8101 multibeam echosounders, as well as 234-kHz and 468-kHz SEA SWATHplus 

bathymetric sidescan-sonar systems. These mapping missions combined to collect both bathymetry 

(sheets 1, 2) and acoustic-backscatter data (sheet 3) from about the 10-m isobath to beyond the 3-

nautical-mile limit of California’s State Waters.

During the Fugro Pelagos and CSUMB mapping missions, an Applanix POS MV (Position and 

Orientation System for Marine Vessels) was used to accurately position the vessels during data 

collection, and it also accounted for vessel motion such as heave, pitch, and roll (position accuracy, ±2 

m; pitch, roll, and heading accuracy, ±0.02°; heave accuracy, ±5%, or 5 cm). To account for tidal-cycle 

fluctuations, CSUMB used NavCom 2050 GPS receiver (CNAV) data, and Fugro Pelagos used KGPS 

data (GPS data with real-time kinematic corrections); in addition, sound-velocity profiles were collected 

with an Applied Microsystems (AM) SVPlus sound velocimeter. Soundings were corrected for vessel 

motion using the Applanix POS MV data, for variations in water-column sound velocity using the AM 

SVPlus data, and for variations in water height (tides) using vertical-position data from the KGPS 

receivers. 

The multibeam-echosounder backscatter data were postprocessed using Geocoder within Caris 

HIPS and SIPS software. Within Geocoder, the backscatter intensities were radiometrically corrected 

(including despeckling and angle-varying gain adjustments), and the position of each acoustic sample 

was geometrically corrected for slant range on a line-by-line basis. After the lines were corrected, they

were mosaicked together into 1- or 2-m-resolution images. Overlap between parallel lines was resolved 

using a priority table whose values were based on the distance of each sample from the ship track, with 

the samples that were closest to and furthest from the ship track being given the lowest priority. An antialiasing algorithm was also applied. The mosaics were then exported as georeferenced TIFF images, 

imported into a geographic information system (GIS), and converted to GRIDs at 2-m resolution. 

During the USGS mapping mission within Tomales Bay (Anima and others, 2008), differential 

GPS (DGPS) data were combined with measurements of vessel motion (heave, pitch, and roll) in a 

CodaOctopus F180 attitude-and-position system to produce a high-precision vessel-attitude packet. This 

packet was transmitted to the acquisition software in real time and combined with instantaneous soundvelocity measurements at the transducer head before each ping. The returned samples were projected to 

the seafloor using a ray-tracing algorithm that works with previously measured sound-velocity profiles. 

Statistical filters were applied to the raw samples that discriminate the seafloor returns (soundings) from 

unintended targets in the water column. Finally, the soundings were converted into 2-m-resolution 

bathymetric-surface-model grids. The backscatter data were postprocessed using USGS software (D.P. 

Finlayson, written commun., 2011) that normalizes for time-varying signal loss and beam-directivity 

differences. Thus, the raw 16-bit backscatter data were gain-normalized to enhance the backscatter of 
9

the SWATHplus system. The resulting normalized-amplitude values were rescaled to 16-bit and gridded 

into GeoJPEGs using GRID Processor Software, then imported into a GIS and converted to GRIDs. 

Processed soundings from the different mapping missions were exported from the acquisition or 

processing software as XYZ files and bathymetric surfaces. All the surfaces were merged into one 

overall 2-m-resolution bathymetric-surface model and clipped to the boundary of the map area. An 

illumination having an azimuth of 300° and from 45° above the horizon was then applied to the 

bathymetric surface to create the shaded-relief imagery (sheets 1, 2). In addition, a modified “rainbow” 

color ramp was applied to the bathymetry data for sheet 1, using reds and oranges to represent shallower 

depths, and greens to represent greater depths (note that the Offshore of Tomales Point map area 

requires only the shallower part of the full-rainbow color ramp used on some of the other maps in the 

California State Waters Map Series; see, for example, Kvitek and others, 2012). This colored 

bathymetry surface was draped over the shaded-relief imagery at 60-percent transparency to create a 

colored shaded-relief map (sheet 1). Note that the ripple patterns and straight lines that are apparent 

within the map area are data-collection artifacts. In addition, lines at the borders of some surveys are the 

result of slight differences in depth, as measured by different mapping systems in different years. These 

various artifacts are made obvious by the hillshading process. 

Bathymetric contours (sheets 1, 2, 3, 7, and 10) were generated at 10-m intervals from a 

modified 2-m-resolution bathymetric surface. The original surface was smoothed using the Focal Mean 

tool in ArcGIS and a circular neighborhood with a radius of 20 to 30 m (depending on the area). The 

contours were generated from this smoothed surface using the ArcGIS Spatial Analyst Contour tool. The 

most continuous contour segments were preserved; smaller segments and isolated island polygons were 

excluded from the final output. Contours were smoothed using a polynomial approximation with 

exponential kernel algorithm and a tolerance value of 60 m. 

The acoustic-backscatter imagery from each different mapping system and processing method 

were merged into their own individual grids. These individual grids, which cover different areas, were 

displayed in a GIS to create an acoustic-backscatter map (sheet 3). On the map, brighter tones indicate 

higher backscatter intensity, and darker tones indicate lower backscatter intensity. The intensity 

represents a complex interaction between the acoustic pulse and the seafloor, as well as characteristics 

within the shallow subsurface, providing a general indication of seafloor texture and sediment type. 

Backscatter intensity depends on the acoustic source level; the frequency used to image the seafloor; the 

grazing angle; the composition and character of the seafloor, including grain size, water content, bulk 

density, and seafloor roughness; and some biological cover. Harder and rougher bottom types such as 

rocky outcrops or coarse sediment typically return stronger intensities (high backscatter, lighter tones), 

whereas softer bottom types such as fine sediment return weaker intensities (low backscatter, darker 

tones). 

The onshore-area image was generated by applying an illumination having an azimuth of 300° 

and from 45° above the horizon to 2- and 3-m-resolution topographic-lidar data available from NOAA 

Coastal Service Center’s Digital Coast (available at http://coast.noaa.gov/digitalcoast/) and from the 

U.S. Geological Survey’s National Elevation Dataset (available at http://ned.usgs.gov/). 
10

Chapter 3. Data Integration and Visualization for the Offshore of 

Tomales Point Map Area (Sheet 4) 

By Peter Dartnell

Mapping California’s State Waters has produced a vast amount of acoustic and visual data, 

including bathymetry, acoustic backscatter, seismic-reflection profiles, and seafloor video and 

photography. Researchers use these data to develop maps, reports, and other tools to assist coastal-zone 

managers and other stakeholders in coastal and marine spatial-planning. For example, seafloor-character 

(sheet 5), habitat (sheet 7), and geologic (sheet 10) maps of the Offshore of Tomales Point map area may 

assist in the designation of Marine Protected Areas, as well as in their monitoring. These maps and 

reports also help to analyze environmental change owing to sea-level rise and coastal development, to 

model and predict sediment and contaminant budgets and transport, to site offshore infrastructure, and to 

assess tsunami and earthquake hazards. To facilitate this increased understanding and to assist in product 

development, it is helpful to integrate the different datasets and then view the results in threedimensional representations such as those displayed on the data integration and visualization sheet for 

the Offshore of Tomales Point map area (sheet 4). 

The maps and three-dimensional views on sheet 4 were created using a series of geographic 

information systems (GIS) and visualization techniques. Using GIS, the bathymetric and topographic 

data (sheet 1) were converted to ASCIIRASTER format files, and the acoustic-backscatter data (sheet 3) 

were converted to geoTIFF images. The bathymetric and topographic data were imported in the 

Fledermaus® software (QPS). The bathymetry was color-coded to closely match the colored shadedrelief bathymetry on sheet 1 in which reds and oranges represent shallower depths and blues represent 

deeper depths. Topographic data were shown in gray shades. The acoustic-backscatter geoTIFF images 

were also draped over the bathymetry data. The colored bathymetry, topography, and draped backscatter 

were then tilted and panned to create the perspective views such as those shown in figures 1 through 6 

on sheet 4. These figures highlight the seafloor morphology in the Offshore Tomales Point map area, 

which includes outcrops of fractured bedrock and complex patterns of shallow depressions. 

Video-mosaic images created from digital seafloor video (for example, fig. 4 on sheet 4) display 

the geologic complexity (rock, sand, and mud; see sheet 10) and biologic complexity (see sheet 6) of the 

seafloor. Whereas photographs capture high-quality snapshots of smaller areas of the seafloor (see sheet 

6), video mosaics capture larger areas and can show transition zones between seafloor environments. 

Digital seafloor video is collected from a camera sled towed approximately 1 to 2 meters above the 

seafloor, at speeds of less than 1 nautical mile/hour. Using standard video-editing software, as well as 

software developed at the Center for Coastal and Ocean Mapping, University of New Hampshire, the 

digital video is converted to AVI format, cut into 2-minute sections, and desampled to every second or 

third frame. The frames are merged together using pattern-recognition algorithms from one frame to the 

next and converted to a TIFF image. The images are then rectified to the bathymetry data using ship 

navigation recorded with the video and layback estimates of the towed camera sled. 

Block diagrams that combine the bathymetry and backscatter with seismic-reflection-profile data 

help integrate surface and subsurface observations, especially stratigraphic and structural relations (for 

example, fig. 6 on sheet 4). These block diagrams were created by converting digital seismic-reflectionprofile data (see sheet 8) into TIFF images, while taking note of the starting and ending coordinates and 

maximum and minimum depths. The images were then imported into the Fledermaus® software as 

vertical images and merged with the bathymetry imagery.
11

Chapter 4. Seafloor-Character Map of the Offshore of Tomales Point 

Map Area (Sheet 5)

By Mercedes D. Erdey and Guy R. Cochrane

The California State Marine Life Protection Act (MLPA) calls for protecting representative types 

of habitat in different depth zones and environmental conditions. A science team, assembled under the 

auspices of the California Department of Fish and Wildlife (CDFW), has identified seven substratedefined seafloor habitats in California’s State Waters that can be classified using sonar data and seafloor 

video and photography. These habitats include rocky banks, intertidal zones, sandy or soft ocean 

bottoms, underwater pinnacles, kelp forests, submarine canyons, and seagrass beds. The following five 

depth zones, which determine changes in species composition, have been identified: Depth Zone 1, 

intertidal; Depth Zone 2, intertidal to 30 m; Depth Zone 3, 30 to 100 m; Depth Zone 4, 100 to 200 m; 

and Depth Zone 5, deeper than 200 m (California Department of Fish and Wildlife, 2008). The CDFW 

habitats, with the exception of depth zones, can be considered a subset of a broader classification 

scheme of Greene and others (1999) that has been used by the U.S. Geological Survey (USGS) 

(Cochrane and others, 2003, 2005). These seafloor-character maps are generalized polygon shapefiles 

that have attributes derived from Greene and others (2007). 

A 2007 Coastal Map Development Workshop, hosted by the USGS in Menlo Park, California, 

identified the need for more detailed (relative to Greene and others’ [1999] attributes) raster products 

that preserve some of the transitional character of the seafloor when substrates are mixed and (or) they 

change gradationally. The seafloor-character map, which delineates a subset of the CDFW habitats, is a 

GIS-derived raster product that can be produced in a consistent manner from data of variable quality 

covering large geographic regions.

The following four substrate classes are identified in the Offshore of Tomales Point map area: 

• Class I: Fine- to medium-grained smooth sediment

• Class II: Mixed smooth sediment and rock 

• Class III: Rock and boulder, rugose 

• Class IV: Medium- to coarse-grained sediment (in scour depressions) 

The seafloor-character map of the Offshore of Tomales Point map area (sheet 5) was produced 

using video-supervised maximum-likelihood classification of the bathymetry and intensity of return 

from sonar systems, following the method described by Cochrane (2008). The two variants used in this 

classification were backscatter intensity and derivative rugosity. Rugosity calculation was performed 

using the Terrain Ruggedness (VRM) tool within the Benthic Terrain Modeler toolset v. 3.0 (Wright and 

others, 2012; available at http://esriurl.com/5754).

Classes I, II, and III values were delineated using multivariate analysis. Class IV (medium- to 

coarse-grained sediment, in scour depressions) values were determined on the basis of their visual 

characteristics using both shaded-relief bathymetry and backscatter (slight depression in the seafloor, 

very high backscatter return). The resulting map (gridded at 2 m) was cleaned by hand to remove data 

collection artifacts (for example, the trackline nadir).

On the seafloor-character map (sheet 5), the four substrate classes have been colored to indicate 

the California MLPA depth zones and the Coastal and Marine Ecological Classification Standard 

(CMECS) slope zones (Madden and others, 2008) in which they belong. The California MLPA depth 

zones are Depth Zone 1 (intertidal), Depth Zone 2 (intertidal to 30 m), Depth Zone 3 (30 to 100 m), 
12

Depth Zone 4 (100 to 200 m), and Depth Zone 5 (greater than 200 m); in the Offshore Tomales Point 

map area, only Depth Zones 2 and 3 are present. The slope classes that represent the CMECS slope 

zones are Slope Class 1 = flat (0° to 5°), Slope Class 2 = sloping (5° to 30°), Slope Class 3 = steeply 

sloping (30° to 60°), Slope Class 4 = vertical (60° to 90°), and Slope Class 5 = overhang (greater than 

90°); in the Offshore Tomales Point map area, only Slope Classes 1 and 2 are present. The final 

classified seafloor-character raster map image has been draped over the shaded-relief bathymetry for the 

area (sheets 1 and 2) to produce the image shown on the seafloor-character map on sheet 5.

The seafloor-character classification also is summarized on sheet 5 in table 1. Fine- to mediumgrained smooth sediment (sand and mud) makes up 56.5 percent (71.7 km2

) of the map area: 14.3 

percent (18.2 km2

) is in Depth Zone 2, and 42.2 percent (53.5 km2) is in Depth Zone 3. Mixed smooth 

sediment (sand and gravel) and rock (that is, sediment typically forming a veneer over bedrock, or rock 

outcrops having little to no relief) make up 23.9 percent (30.2 km2

) of the map area: 4.2 percent (5.3 

km2

) is in Depth Zone 2, and 19.7 percent (24.9 km2) is in Depth Zone 3. Rock and boulder, rugose 

(rock and boulder outcrops having high surficial complexity) makes up 14.4 percent (18.2 km2) of the 

map area: 6.9 percent (8.7 km2) is in Depth Zone 2, and 7.5 percent (9.5 km2) is in Depth Zone 3. 

Medium- to coarse-grained sediment (in scour depressions consisting of material that is coarser than the 

surrounding seafloor) makes up 5.2 percent (6.6 km2) of the map area: 0.8 percent (1.0 km2) is in Depth 

Zone 2 and 4.4 percent (5.6 km2) is in Depth Zone 3. 

A small number of video observations were used to supervise the numerical classification of the 

seafloor. All video observations (see sheet 6) are used for accuracy assessment of the seafloor-character 

map after classification. To compare observations to classified pixels, each observation point is assigned 

a class (I, II, or III), according to the visually derived, major or minor geologic component (for example, 

sand or rock) and the abiotic complexity (vertical variability) of the substrate recorded during groundtruth surveys (table 4–1; see also, chapter 5 of this pamphlet). Class IV values were assigned on the 

basis of the observation of one or more of a group of features that includes both larger scale bedforms 

(for example, sand waves), as well as sediment-filled scour depressions that resemble the “rippled scour 

depressions” of Cacchione and others (1984) and Phillips and others (2007) and also the “sorted 

bedforms” of Murray and Thieler (2004), Goff and others (2005), and Trembanis and Hume (2011). On 

the geologic map (see sheet 10 of this report), they are referred to as “marine shelf scour depressions.” 

Next, circular buffer areas were created around individual observation points using a 10-m radius 

to account for layback and positional inaccuracies inherent to the towed-camera system. The radius 

length is an average of the distances between the positions of sharp interfaces seen on both the video 

(the position of the ship at the time of observation) and sonar data, plus the distance covered during a 

10-second observation period at an average speed of 1 nautical mile/hour. Each buffer, which covers 

more than 300 m2

, contains approximately 77 pixels. The classified (I, II, III) buffer is used as a mask to 

extract pixels from the seafloor-character map. These pixels are then compared to the class of the buffer. 

For example, if the shipboard-video observation is Class II (mixed smooth sediment and rock), but 12 of 

the 77 pixels within the buffer area are characterized as Class I (fine- to medium-grained smooth 

sediment), and 15 (of the 77) are characterized as Class III (rock and boulder, rugose), then the 

comparison would be “Class I, 12; Class II, 50; Class III, 15” (fig. 4–1). If the video observation of 

substrate is Class II, then the classification is accurate because the majority of seafloor pixels in the 

buffer are Class II. The accuracy values in table 4–2 represent the final of several classification 

iterations aimed at achieving the best accuracy, given the variable quality of sonar data (see discussion 

in Cochrane, 2008) and the limited ground-truth information available when compared to the continuous 

coverage provided by swath sonar. Presence/absence values in table 4–2 reflect the percentages of 
13

observations where the sediment classification of at least one pixel within the buffer zone agreed with 

the observed sediment type at a certain location. 

The seafloor in the Offshore of Tomales Point map area is complex, dominated by fractured and 

folded, rugose bedrock outcrops (Class III). The rock outcrops are covered with varying thicknesses of 

fine (Class I) to coarse (Class II) sediment. Several areas of medium- to coarse-grained scour 

depressions (Class IV) have also been identified adjacent to rock outcrops. The Tomales Bay inlet is 

dominated by Class I sediments of sand and mud and large sandwaves formed by coarser sand (Class 

IV).

Due to the mixture of different sediments covering the seafloor within this map area, the 

classification accuracy is found to be somewhat lower than for other areas we have mapped in 

California’s State Waters, as determined by comparing the shipboard video observations and the 

classified map—53 percent accurate for Class I, 49 percent accurate for Class II, 38 percent accurate for 

Class III, and 46 percent accurate for Class IV. Coarser sediments accumulated in seafloor depressions 

(Class IV) often form megaripples, which might not be always recognizable on the video footage 

especially when visibility is limited. Bedrock outcrops in this area are composed of differentially eroded 

sedimentary rocks (Cochrane and Lafferty, 2002). Erosion of softer layers produces Class I and II 

sediments, resulting in patchy areas of rugose rock and boulder habitat (Class III) on the seafloor. The 

lower classification accuracy in all classes is likely due to the relatively narrow and intermittent nature 

of transition zones (from fine to coarse sediment to rock), relative to the observation buffer size. A 

single buffered observation locale of 78 pixels, therefore, is likely to be interspersed with other classes 

of pixels, in addition to Class III. Percentages for presence/absence within a buffer also were calculated 

as a better measure of the accuracy of the classification for patchy rock habitat. The presence/absence 

accuracy was found to be significant for all classes (76 percent for Class I, 76 percent for Class II, 76 

percent for Class III, and 55 percent for Class IV).

 

Figure 4–1. Detailed view of ground-truth data, showing accuracy-assessment methodology. A, Dots illustrate 

ground-truth observation points, each of which represents 10-second window of substrate observation plotted 

over seafloor-character grid; circle around dot illustrates area of buffer depicted in B. B, Pixels of seafloorcharacter data within 10-m-radius buffer centered on one individual ground-truth video observation.
14

Table 4–1. Conversion table showing how video observations of primary substrate (more than 50 percent seafloor 

coverage), secondary substrate (more than 20 percent seafloor coverage), and abiotic seafloor complexity (in 

first three columns) are grouped into seafloor-character-map Classes I, II, and III for use in supervised 

classification and accuracy assessment in Offshore of Tomales Point map area. 

[In areas of low visibility where primary and secondary substrate could not be identified with confidence, recorded observations of 

substrate (in fourth column) were used to assess accuracy]

Primary-substrate component Secondary-substrate component Abiotic seafloor complexity Low-visibility observations

Class I

mud mud low 

mud sand low 

sand mud low 

sand mud moderate 

sand sand low 

sand sand moderate

sediment

mud component

ripples

Class II

boulders sand low

cobbles sand low

gravel mud low

mud cobbles low

rock boulders low

rock rock low

rock sand low

sand cobbles low 

sand cobbles moderate

sand gravel low 

sand gravel moderate

sand rock low

sand rock moderate

Class III

boulders boulders moderate

boulders boulders high

boulders cobbles moderate

boulders mud moderate

boulders rock moderate

boulders rock high

boulders sand moderate

cobbles boulders moderate
15

Primary-substrate component Secondary-substrate component Abiotic seafloor complexity Low-visibility observations

cobbles sand moderate

mud boulders moderate

sand boulders moderate

rock boulders moderate

rock boulders high

rock cobbles moderate

rock mud moderate

rock rock moderate

rock rock high

rock sand moderate

rock sand high

Class IV

sand sand low

sand sand moderate

megaripples

oscillatory megaripples

depression

Table 4–2. Accuracy-assessment statistics for seafloor-character-map classifications in Offshore of Tomales Point 

map area.

[Accuracy assessments are based on video observations]

Class Number of observations % majority % presence/absence

I—Fine- to medium-grained smooth sediment 216 53.4 76.4

II—Mixed smooth sediment and rock 172 49.0 76.2

III—Rock and boulder, rugose 239 38.0 76.2

IV—Medium- to coarse-grained sediment (in scour 

depressions) 42 45.8 54.8

 
16

Chapter 5. Ground-Truth Studies for the Offshore of Tomales Point Map 

Area (Sheet 6)

By Nadine E. Golden and Guy R. Cochrane 

To validate the interpretations of sonar data in order to turn it into geologically and biologically 

useful information, the U.S. Geological Survey (USGS) towed a camera sled (fig. 5–1) over specific 

locations throughout the Offshore of Tomales Point map area to collect video and photographic data that 

would “ground truth” the seafloor. This ground-truth surveying occurred in 2008. The camera sled was 

towed 1 to 2 m above the seafloor at speeds of between 1 and 2 nautical miles/hour. Ground-truth 

surveys in this map area include approximately 11 trackline kilometers of video and 547 still 

photographs, in addition to 731 recorded seafloor observations of abiotic and biotic attributes. A visual 

estimate of slope also was recorded.

Figure 5–1. Photograph of camera sled used in USGS 2008 ground-truth survey.

During the cruise, the USGS camera sled housed two standard-definition (640×480 pixel 

resolution) video cameras (one forward looking, and the other downward looking), a high-definition 

(1,080×1,920 pixel resolution) video camera, and an 8-megapixel digital still camera. During this cruise, 

in addition to recording the seafloor characteristics, a digital still photograph was captured once every 30 

seconds. 

The camera-sled tracklines (shown by colored dots on the map on sheet 6) are sited in order to 

visually inspect areas representative of the full range of bottom hardness and rugosity in the map area. 

The video is fed in real time to the research vessel, where USGS and National Oceanic and Atmospheric 

Administration (NOAA) scientists record both the geologic and biologic character of the seafloor. While 

the camera is deployed, several different observations are recorded for a 10-second period once every 

minute, using the protocol of Anderson and others (2007). Observations of primary substrate, secondary 
17

substrate, slope, abiotic complexity, biotic complexity, and biotic cover are mandatory. Observations of 

key geologic features and the presence of key species also are made. 

Primary and secondary substrate, by definition, constitute greater than 50 and 20 percent of the 

seafloor, respectively, during an observation. The grain-size values that differentiate the substrate 

classes are based on the Wentworth (1922) scale, and the sand, cobble, and boulder sizes are classified 

as in Wentworth (1922). However, the difficulty in distinguishing the finest divisions in the Wentworth 

(1922) scale during video observations made it necessary to aggregate some grain-size classes, as was 

done in the Anderson and others (2007) methodology: the granule and pebble sizes have been grouped 

together into a class called “gravel,” and the clay and silt sizes have been grouped together into a class 

called “mud.” In addition, hard bottom and clasts larger than boulder size are classified as “rock.” 

Benthic-habitat complexity, which is divided into abiotic (geologic) and biotic (biologic) components, 

refers to the visual classification of local geologic features and biota that potentially can provide refuge 

for both juvenile and adult forms of various species (Tissot and others, 2006). 

Sheet 6 contains a smaller, simplified (depth-zone symbology has been removed) version of the 

seafloor-character map on sheet 5. On this simplified map, the camera-sled tracklines used to groundtruth-survey the sonar data are shown by aligned colored dots, each dot representing the location of a 

recorded observation. A combination of abiotic attributes (primary- and secondary-substrate 

compositions), as well as vertical variability, were used to derive the different classes represented on the 

seafloor-character map (sheet 5); on the simplified map, the derived classes are represented by colored 

dots. Also on this map are locations of the detailed views of seafloor character, shown by boxes (Boxes 

A through C); for each view, the box shows the locations (indicated by colored stars) of representative 

seafloor photographs. For each photograph, an explanation of the observed seafloor characteristics 

recorded by USGS and NOAA scientists is given. Note that individual photographs often show more 

substrate types than are reported as the primary and secondary substrate. Organisms, when present, are 

labeled on the photographs. 

The ground-truth survey is designed to investigate areas that represent the full spectrum of highresolution multibeam bathymetry and backscatter-intensity variation. Figure 5–2 shows that, in the 

Offshore of Tomales Point map area, the seafloor surface is characterized by patchy distributions of 

sandy sediment and exposed rock. Nearshore areas of rocky habitat are notably present along the waveexposed coast of Tomales Point in the northern half of the map area. Rocks exposed in this area (sheet 6 

on fig. 1J) are massive granitic rocks uplifted along the San Andreas Fault (see also, sheet 10). To the 

south, exposures of layered-sedimentary rock in deeper water are of lower relief, consisting of both 

Class II (fig. 3E on sheet 6) and Class III (fig. 3H on sheet 6) habitat types, indicating differential 

erosion of less resistant layers. The patchy combination of different geologic units across the spectrum 

of depths makes this one of the more diverse habitat areas. 
18

Figure 5–2. Graph showing distribution of primary and secondary substrate determined from video observations in 

Offshore of Tomales Point map area.
19

Chapter 6. Potential Marine Benthic Habitats of the Offshore of Tomales 

Point Map Area (Sheet 7)

By H. Gary Greene, Charles A. Endris, and Bryan E. Dieter

The map on sheet 7 shows “potential” marine benthic habitats in the Offshore of Tomales Point 

map area, representing a substrate type, geomorphology, seafloor process, or any other attribute that may 

provide a habitat for a specific species or assemblage of organisms. This map, which is based largely on 

seafloor geology, also integrates information displayed on several other thematic maps of the Offshore 

of Tomales Point map area. High-resolution sonar bathymetry data, converted to depth grids (seafloor 

DEMs; sheet 1), are essential to development of the potential marine benthic habitat map, as is shadedrelief imagery (sheet 2), which allows visualization of seafloor terrain and provides a foundation for 

interpretation of submarine landforms. 

Backscatter maps (sheet 3) also are essential for developing potential benthic habitat maps. High 

backscatter is further indication of “hard” bottom, consistent with interpretation as rock or coarse 

sediment. Low backscatter, indicative of a “soft” bottom, generally indicates a fine-sediment 

environment. Habitat interpretations also are informed by actual seafloor observations from ground-truth 

surveying (sheet 6), by seafloor-character maps that are based on video-supervised maximum-likelihood 

classification (sheet 5), and by seafloor-geology maps (sheet 10). The habitat interpretations on sheet 7 

are further informed by the usSEABED bottom-sampling compilation of Reid and others (2006). 

Broad, generally smooth areas of seafloor that lack sharp and angular edge characteristics are 

mapped as “sediment;” these areas may be further defined by various sedimentary features (for example, 

erosional scours and depressions) and (or) depositional features (for example, dunes, mounds, or sand 

waves). In contrast, many areas of seafloor bedrock exposures are identified by their common sharp 

edges and high relative relief; these may be contiguous outcrops, isolated parts of outcrop protruding 

through sediment cover (pinnacles or knobs), or isolated boulders. In many locations, areas within or 

around a rocky feature appear to be covered by a thin veneer of sediment; these areas are identified on 

the habitat map as “mixed” induration (that is, containing both rock and sediment). The combination of 

remotely observed data (for example, high-resolution bathymetry and backscatter, seismic-reflection 

profiles) and directly observed data (for example, camera transects, sediment samples) translates to 

higher confidence in the ability to interpret broad areas of the seafloor. 

To avoid any possible misunderstanding of the term “habitat,” the term “potential habitat” (as 

defined by Greene and others, 2005) is used herein to describe a set of distinct seafloor conditions that in 

the future may qualify as an “actual habitat.” Once habitat associations of a species are determined, they 

can be used to create maps that depict actual habitats, which then need to be confirmed by in situ

observations, video, and (or) photographic documentation. 

Classifying Potential Marine Benthic Habitats

Potential marine benthic habitats in the Offshore of Tomales Point map area are mapped using 

the Benthic Marine Potential Habitat Classification Scheme, a mapping-attribute code developed by 

Greene and others (1999, 2007). This code, which has been used previously in other offshore California 

areas (see, for example, Greene and others, 2005, 2007), was developed to easily create categories of 

marine benthic habitats that can then be queried within a GIS or a database. The code contains several 

categories that can be subdivided relative to the spatial scale of the data. The following categories can be 

applied directly to habitat interpretations determined from remote-sensing imagery collected at a scale of 
20

tens of kilometers to one meter: Megahabitat, Seafloor Induration, Meso/Macrohabitat, Modifier, 

Seafloor Slope, Seafloor Complexity, and Geologic Unit. Additional categories of Macro/Microhabitat, 

Seafloor Slope, Seafloor Complexity, and Geologic Attribute can be applied to habitat interpretations 

determined from seafloor samples, video, still photographs, or direct observations at a scale of 10 meters 

to a few centimeters. These two scale-dependent groups of categories can be used together, to define a 

habitat across spatial scales, or separately, to compare large- and small-scale habitat types. 

The four categories and their attribute codes that are used on the Offshore of Tomales Point map 

are explained in detail below (note, however, that not all categories may be used in a particular map 

area, given the study objectives, data availability, or data quality); attribute codes in each category are 

depicted on the map by the letters and, in some cases, numbers that make up the map-unit symbols: 

Megahabitat—Based on depth and general physiographic boundaries; used to distinguish 

features on a scale of tens of kilometers to kilometers. Depicted on map by capital letter, listed first in 

map-unit symbol; generalized depth ranges are given below: 

E = Estuary (0 to 100 m) 

S = Shelf; continental and island shelves (0 to 200 m) 

Seafloor Induration—Refers to substrate hardness. Depicted on map by lower-case letter, listed 

second in map-unit symbol; may be further subdivided into distinct sediment types, depicted by lowercase letter(s) in parentheses, listed immediately after substrate hardness; multiple attributes listed in 

general order of relative abundance, separated by slash; queried where inferred.

h = Hard bottom (for example, rock outcrop or sediment pavement) 

m = Mixed hard and soft bottom (for example, local sediment cover of bedrock) 

s = Soft bottom; sediment cover

(b) = Boulders 

(g) = Gravel

(s) = Sand

(m) = Mud, silt, and (or) clay

Meso/Macrohabitat—Related to scale of habitat; consists of seafloor features one kilometer to 

one meter in size. Depicted on map by lower-case letter and, in some cases, additional lower-case letter 

in parentheses, listed third in map-unit symbol; multiple attributes separated by slash.

b = Beach, relic (submerged) or shoreline 

(b)/p = Pinnacle indistinguishable from boulder 

d = Deformed, tilted and (or) folded bedrock; overhang 

e = Exposure; bedrock 

h = Hole; depression 

m = Mound; linear ridge 

p = Pinnacle; cone 

s = Scarp, cliff, fault, or slump scar 

w = Dynamic bedform

y = Delta; fan

Modifier—Describes texture, bedforms, biology, or lithology of seafloor. Depicted on map by 

lower-case letter, in some cases followed by additional lower-case letter(s) either after hyphen or in 

parentheses (or both), following an underscore; multiple attributes separated by slash. 

_a = Anthropogenic (artificial reef, breakwall, shipwreck, disturbance) 

_a-dg = Dredge groove or channel

_a-g = Groin, jetty, rip-rap

_a-w = Wreck, ship, barge, or plane 
21

_c = Consolidated sediment (claystone, mudstone, siltstone, sandstone, breccia, or 

conglomerate) 

_d = Differentially eroded

_f = Fracture, joint; faulted

_g = Granite

_h = Hummocky, irregular relief

_r = Ripple (amplitude, greater than 10 cm) 

_s = Scour (current or ice; direction noted) 

_u = Unconsolidated sediment 

Examples of Attribute Coding

To illustrate how these attribute codes can be used to describe remotely sensed data, the 

following examples are given: 

Ss(s)_u = Soft unconsolidated sediment (sand) on continental shelf. 

Es(s/m)_r/u = Ripples, soft, unconsolidated sediment (sand and mud) in estuary. 

She_g = Hard rock outcrop (granite) on continental shelf. 

Map Area Habitats

Delineated in the Offshore of Tomales Point map area are 23 potential marine benthic habitat 

types, covering 126.97 km2

. These include unconsolidated sediments, mixed substrate, hard substrate, 

and possible anthropogenic features on the continental shelf, as well as unconsolidated sediments and 

mixed substrate in the estuary. The habitat types mapped on the shelf cover an area of 117.22 km2

 (92.3 

percent) while those in the estuary (Tomales Bay) cover 9.75 km2 (7.7 percent). In the total area mapped 

(shelf and estuary), the predominant habitat type is soft unconsolidated sediment, covering 85.30 km2

(67.2 percent). Exposed hard bedrock covers 37.34 km2 (29.4 percent); sediment-covered bedrock, 

which is of the mixed hard-soft induration class, covers 4.21 km2

 (3.3 percent); hard, unidentified 

anthropogenic features, possibly related to marine debris, covers 0.13 km2 (0.1 percent). 

Rock outcrops and rubble are considered the primary habitat types for rockfish and lingcod (Cass 

and others, 1990; Love and others, 2002), both of which are recreationally and commercially important 

species. Dynamic bedforms such as sand waves are considered potential foraging habitat for juvenile 

lingcod (Ophiodon elongatus) and possibly migratory fishes (Beaudreau, 2005), as well as for forage 

fish such as Pacific sand lance.
22

Chapter 7. Subsurface Geology and Structure of the Offshore of 

Tomales Point Map Area and the Salt Point to Drakes Bay Region 

(Sheets 8 and 9)

By Samuel Y. Johnson, Stephen R. Hartwell, Janet T. Watt, Ray W. Sliter, and John L. Chin 

The seismic-reflection profiles presented on sheet 8 provide a third dimension, depth, to 

complement the surficial seafloor-mapping data already presented (sheets 1 through 7) for the Offshore 

of Tomales Point map area. These data, which are collected at two resolutions, extend to varying depths 

in the subsurface, depending on the purpose and mode of data acquisition. The seismic-reflection 

profiles (sheet 8) provide information on sediment character, distribution, and thickness, as well as 

potential geologic hazards, including active faults, areas prone to strong ground motion, and 

tsunamigenic slope failures. The information on faults provides essential input to national and state 

earthquake-hazard maps and assessments (for example, Petersen and others, 2008). 

The maps on sheet 9 show the following interpretations, which are based on the seismicreflection profiles on sheet 8: the thickness of the uppermost sediment unit; the depth to base of this 

uppermost unit; and both the local and regional distribution of faults and earthquake epicenters (data 

from U.S. Geological Survey and California Geological Survey, 2010; Northern California Earthquake 

Data Center, 2014). 

Data Acquisition

Most profiles displayed on sheet 8 (figs. 1, 2, 3, 4, 6, and 7) were collected in 2009 on U.S. 

Geological Survey (USGS) cruise S–8–09–NC. The single-channel seismic-reflection data were 

acquired using the SIG 2Mille minisparker that used a 500-J high-voltage electrical discharge fired 1 to 

4 times per second, which, at normal survey speed of 4 to 4.5 nautical miles/hour, gives a data trace 

every 0.5 to 2.0 m of lateral distance covered. The data were digitally recorded in standard SEG-Y 32-

bit floating-point format, using Triton Subbottom Logger (SBL) software that merges seismic-reflection 

data with differential GPS-navigation data. After the survey, a short-window (20 ms) automatic gain 

control algorithm was applied to the data, along with a 160- to 1,200-Hz bandpass filter and a heave 

correction that uses an automatic seafloor-detection window (averaged over 30 m of lateral distance 

covered). These high-resolution data can resolve geologic features that are a few meters thick (smallscale features) to subbottom depths of as much as a few hundred meters. 

Figure 5 on sheet 8 shows a deep-penetration, migrated, multichannel seismic-reflection profile 

collected in 1976 by WesternGeco on cruise W–14–76–SF. This profile and other similar data were 

collected in many areas offshore of California in the 1970s and 1980s when these areas were considered 

a frontier for oil and gas exploration. Most of these data have been publicly released and are now 

archived at the U.S. Geological Survey National Archive of Marine Seismic Surveys (U.S. Geological 

Survey, 2009). These data were acquired using a large-volume air-gun source that has a frequency range 

of 3 to 40 Hz and recorded using a multichannel hydrophone streamer about 2 km long. Shot spacing 

was about 30 m. These data can resolve geologic features that are 20 to 30 m thick, down to subbottom 

depths of about 4 km. 
23

Seismic-Reflection Imaging of the Continental Shelf

Sheet 8 shows seismic-reflection profiles in the Offshore of Tomales Point map area. The 

northwest-trending San Andreas Fault strikes through Tomales Bay in the northeastern part of the map 

area. Fault slip along the San Andreas Fault has uplifted Cretaceous granitic rock and overlying folded, 

Neogene marine sedimentary forming Tomales Point and much of the rugged, rocky, continental shelf 

on its west flank. These two different rock types are mapped on the seafloor (sheet 10) based on their 

distinctive surface morphology. Granitic seafloor outcrops are characterized by a massive hackly texture 

and are cut by dense networks of crosscutting fractures and small faults. In contrast, folded Neogene 

sedimentary rocks are characterized by a “ribbed” seafloor morphology, which results from dipping beds 

(lithologies) having variable resistance to erosion. In the southern part of the map area offshore of 

Abbots Lagoon (fig. 1–2), sedimentary rocks are less “ribbed,” owing to shallower dips and more 

uniform lithologies (sheet 10). Seafloor underlain by granitic rocks typically slopes more than 1°, 

whereas the seafloor underlain by sedimentary rocks slopes about 0.5°. 

On seismic-reflection data, the granitic rocks are notably “reflection-free,” whereas the 

sedimentary rocks are characterized by continuous, parallel to subparallel, variable amplitude, highfrequency reflections (terminology after Mitchum and others, 1977). Within the sedimentary rocks, 

intrastratal low-angle unconformities and broad (as wide as about 1 km) channels are common (for 

example, figs. 3, 4, 6 on sheet 8). Lenses of chaotic reflections (for example, figs. 3, 4 on sheet 8) 

primarily consist of the internally deformed fill of small-scale channels. 

Surficial and shallow sediments were deposited in the last about 21,000 years during the sealevel rise that followed the Last Glacial Maximum (LGM) and the last major lowstand (Fairbanks, 1989; 

Fleming and others, 1998; Lambeck and Chappell, 2001; Peltier and Fairbanks, 2006). Sea level was 

about 125 m lower during the LGM, at which time the Offshore of Tomales Point map area was 

emergent, and the shoreline was about 30 km west of its present location. The post-LGM sea-level rise 

was rapid (about 9 to 11 m per thousand years) until about 7,000 years ago, when it slowed considerably 

to about 1 m per thousand years (Peltier and Fairbanks, 2006; Stanford and others, 2011). Sea-level rise 

led to broadening of the continental shelf, progressive eastward migration of the shoreline and wave-cut 

platform, and associated transgressive erosion and deposition. 

The sediments deposited during the post-LGM sea-level rise (the rapid transgression and 

highstand) are shaded blue in the high-resolution seismic-reflection profiles on sheet 8 (figs. 1, 2, 3, 4, 6) 

and their thickness is shown on sheet 9 (Maps B, D). The contact between underlying granitic and 

sedimentary bedrock and post-LGM sediment is an abrupt transgressive surface of erosion (see, for 

example, Catuneanu, 2006), commonly marked by minor channeling, and a common upward change to 

lower amplitude, more diffuse reflections. 

Geologic Structure and Recent Deformation

Faults in the offshore part of the map area are identified on seismic-reflection profiles on the 

basis of the abrupt truncation or warping of reflections and (or) the juxtaposition of reflection panels that 

have differing seismic parameters, such as reflection presence, amplitude, frequency, geometry, 

continuity, and vertical sequence. Most of the map area lies southwest of the right-lateral San Andreas 

Fault Zone, a transform boundary between the North American and Pacific tectonic plates. The San 

Andreas Fault strikes through Tomales Bay (sheet 10), and only the western part of the zone is imaged 

on one seismic-reflection profile in the map area (sheet 8, fig. 1); the profile reveals a down-dropped 

sedimentary basin in the fault zone, bounded to the west by uplifted granitic rocks. Nearby, onland 
24

geologic studies along this section of the San Andreas Fault suggest a slip rate of 17 to 30 mm/yr 

(Bryant and Lundberg, 2002; Grove and Niemi, 2005). 

Both the high-resolution bathymetry (sheets 1, 2) and the seismic-reflection data (sheet 8) reveal 

complex structure beneath the bedrock shelf west of Tomales Point. Numerous northwest-striking faults 

cut both granitic and sedimentary rocks, and their depositional contacts (sheet 8, figs. 1, 6; sheet 10). 

Folds axes trend west to northwest and folds have common wavelengths of 0.5 to 2 kilometers. The 

folding occurred during the late Pliocene or Pleistocene; it does not obviously involve post-LGM 

sediments, and the upper Miocene and Pliocene Purisima Formation is apparently the youngest folded 

unit (Clark and Brabb, 1997). Folding may be synchronous with activity on the northwest-trending Point 

Reyes Thrust Fault which lies about 16 km offshore of the map area (McCulloch, 1987; Heck and 

others, 1990; also see sheet 10, fig. 1). 

Map E on sheet 9 shows the regional pattern of major faults and earthquakes. Fault location is 

simplified and compiled from our mapping within California’s State Waters (see sheet 10), McCulloch 

(1987), and from the U.S. Geological Survey’s Quaternary fault and fold database (U.S. Geological 

Survey and California Geological Survey, 2010). Earthquake epicenters are from the Northern 

California Earthquake Data Center (2014), which is maintained by the U.S. Geological Survey and the 

University of California, Berkeley, Seismological Laboratory; all events of magnitude 2.0 and greater 

for the time period 1967 through March 2014 are shown. The largest earthquake in the map area (M2.1, 

11/18/1978) was located about 5 km west of the Point Reyes Peninsula. A notable lack of 

microseismicity on the adjacent San Andreas Fault has occurred since the devastating great 1906 

California earthquake (M7.8, 4/18/1906), thought to have nucleated on the San Andreas Fault offshore 

of San Francisco (see, for example Bolt, 1968; Lomax, 2005), about 60 km south of the map area. 

Thickness and Depth to Base of Uppermost Pleistocene and Holocene Deposits

Maps on sheet 9 show the thickness and the depth to base of uppermost Pleistocene and 

Holocene (post-LGM) deposits both for the Offshore of Tomales Point map area (Maps A, B) and, to 

establish regional context, for a larger area (about 115 km of coast) that extends from the Salt Point area 

south to the southern part of the Point Reyes peninsula (Maps C, D). To make these maps, water bottom 

and depth to base of the LGM horizons were mapped from seismic-reflection profiles using Seisworks 

software. The difference between the two horizons was exported from Seisworks for every shot point as 

XY coordinates (UTM zone 10) and two-way travel time (TWT). The thickness of the post-LGM unit 

(Maps B, D) was determined by applying a sound velocity of 1,600 m/sec to the TWT, resulting in 

thicknesses as great as about 56 m. The thickness points were interpolated to a preliminary continuous 

surface, overlaid with zero-thickness bedrock outcrops (see sheet 10), and contoured following the 

methodology of Wong and others (2012). 

Several factors required manual editing of the preliminary sediment-thickness maps to make the 

final product. The Gualala, Point Reyes, and San Andreas Faults disrupt the sediment sequence in the 

region (Maps D, E on sheet 9). The thickness data points also are dense along tracklines (about 1 m 

apart) and sparse between tracklines (1 km apart), resulting in minor contouring artifacts. To incorporate 

the effect of the faults, to remove irregularities from interpolation, and to reflect other geologic 

information and complexity, the resulting interpolated contours were modified. Contour modifications 

and regridding were repeated several times to produce the final regional sediment-thickness map (Wong 

and others, 2012). Information for the depth to base of the post-LGM unit (Maps A, C on sheet 9) was 

generated by adding the thickness data to water depths determined by multibeam bathymetry (see sheet 

1). 
25

The thickness of post-LGM unit in the Offshore of Tomales Point map area ranges from 0 to 11 

m (Map B on sheet 9), and the depth to the base of this unit ranges from about 10 m to 85 m (Map A on 

sheet 9). Mean sediment thickness for the map area is 2.3 m and the total sediment volume is 253×106 

m3 (table 7–1). The thickest sediment occurs along the northern map boundary, at the mouth of Tomales 

Bay, and at water depths of about 60 to 75 m due west of Tomales Point. These two areas were once

connected as upper and lower reaches of a now-submerged channel system which provided an outlet for 

local coastal drainages, including what is now Tomales Bay. 

To the south, Cretaceous granitic and Tertiary sedimentary rock crop out on the seafloor or are 

buried by only a thin cover (mostly less than 2.5 m) of uppermost Pleistocene and Holocene sediment. 

This thin sediment cover, in part, results from limited sediment supply. Tomales Point blocks southward 

littoral drift and west-facing coastal watersheds on this part of the Point Reyes Peninsula are very small; 

therefore, much of the relatively meager sediment that is present on the shelf could be derived from 

erosion of local coastal bluffs and sand dunes. The continental shelf offshore of Tomales Point is also 

subject to high wave energy, which has the potential to rework and transport sediment off the shallow to 

midshelf into deeper water. 

Five different “domains” of sediment thickness are recognized on the regional sedimentthickness map (Map D on sheet 9), each with distinctive geologic controls: (1) The Salt Point shelf 

domain, located in the far northwestern part of the region, has a mean sediment thickness of 11.7 m. The 

thickest sediment (20 to 25 m) is found where a pre-LGM, regressive, downlapping sediment wedge 

formed above a break in slope that is controlled by a contact between harder bedrock and softer, folded 

Pleistocene strata. Sediment thinning in this domain within the outer parts of California’s State Waters is 

the result of a relative lack of sediment supply from local watersheds, as well as a more distal Russian 

River source. (2) The Russian River delta and mud belt domain, located offshore of the Russian River, is 

the largest sediment source on this part of the coast and has the thickest uppermost Pleistocene and 

Holocene sediment in the region (mean thickness, 21.1 m). The northward extension of this domain into 

the midshelf “mud belt” results from northward shelf-bottom currents and sediment transport (Drake and 

Cacchione, 1985). This domain includes a section of the San Andreas Fault Zone, which here is 

characterized by several releasing, right-stepping strands that bound narrow, elongate pull-apart basins; 

these sedimentary basins contain the greatest thickness of uppermost Pleistocene and Holocene sediment 

(about 56 m) in the region. (3) The Bodega Head–Tomales Point shelf domain, located between Bodega 

Head and the Point Reyes headland, contains the least amount of sediment in the region (mean 

thickness, 3.4 m). The lack of sediment primarily reflects decreased accommodation space and limited 

sediment supply. (4) The Point Reyes bar domain, located west and south of the Point Reyes headland, 

is a local zone of increased sediment thickness (mean thickness, 14.3 m) created by bar deposition on 

the more protected south flank of the Point Reyes headland during rising sea level. (5) The Bolinas shelf 

domain, located east and southeast of the Point Reyes headland (including most of the Drakes Bay and 

Vicinity map area), has a thin sediment cover (mean thickness, 5.6 m), which likely reflects a limited 

sediment “accommodation space” (Catuneanu, 2006) caused by tectonic uplift (water depths in this 

domain within California’s State Waters are less than 45 m), and high wave energy, capable of 

reworking and transporting shelf sediment to deeper water. 
26

Table 7–1. Area, sediment-thickness, and sediment-volume data for California’s State Waters in Salt Point to

Drakes Bay region (domains 1–5), as well as in Offshore of Tomales Point map area.

Regional sediment-thickness domains in Salt Point to Drakes Bay region

Area (km2) Mean sediment 

thickness (m)

Sediment volume 

(106 m3)

Entire Salt Point to Drakes Bay region 714 9.5 6,794

(1) Salt Point shelf 90 11.7 1,054

(2) Russian River delta and mud belt 144 21.1 3,031

(3) Bodega Head-Tomales Point shelf 275 3.4 928

(4) Point Reyes bar 72 14.3 1,029

(5) Bolinas shelf 133 5.6 752

Sediment thickness in Offshore of Tomales Point map area

Offshore of Tomales Point map area 111 2.3 253
27

Chapter 8. Geologic and Geomorphic Map of the Offshore of Tomales 

Point Map Area (Sheet 10)

By Samuel Y. Johnson, Michael W. Manson, Stephen R. Hartwell, and H. Gary Greene

Geologic and Geomorphic Summary

Marine geology and geomorphology were mapped in the Offshore of Tomales Point map area 

from approximate Mean High Water (MHW) to the 3-nautical-mile limit of California’s State Waters. 

MHW is defined at an elevation of 1.46 m above the North American Vertical Datum of 1988 (NAVD 

88) (Weber and others, 2005). Offshore geologic units were delineated on the basis of integrated 

analyses of adjacent onshore geology with multibeam bathymetry and backscatter imagery (sheets 1, 2, 

3), seafloor-sediment and rock samples (Reid and others, 2006), digital camera and video imagery (sheet 

6), and high-resolution seismic-reflection profiles (sheet 8). Aerial photographs taken in multiple years 

were used to map the nearshore area (0 to 10 m water depth) and to link the offshore and onshore 

geology.

Onshore bedrock mapping is compiled from Galloway (1977), Clark and Brabb (1997), and 

Wagner and Gutierrez (2010). Onshore Quaternary mapping is compiled from Witter and others (2006) 

and Wagner and Gutierrez (2010), with some additional mapping by M.W. Manson (this report); in 

addition, some units are modified by M.W. Manson on the basis of analysis of 2012 lidar imagery. 

Traces of the San Andreas Fault are compiled from California Geological Survey (1974). 

The morphology and the geology of the offshore part of the Offshore of Tomales Point map area 

result from the interplay between tectonics, sea-level rise, local sedimentary processes, and 

oceanography. The map area is cut by the northwest-striking San Andreas Fault, a right-lateral transform 

boundary between the North American and Pacific tectonic plates. The San Andreas Fault strikes 

through Tomales Bay, the northern part of a linear valley that extends from Bolinas through Olema 

Valley to Bodega Bay, which separates mainland California from the Point Reyes Peninsula (fig. 1–1). 

Onshore investigations indicate that this section of the San Andreas Fault has an estimated slip rate of 

about 17 to 25 mm/yr (Bryant and Lundberg, 2002; Grove and Niemi, 2005). The devastating great 1906 

California earthquake (M7.8, 4/18/1906) is thought to have nucleated on the San Andreas Fault about 60 

km south of this map area offshore of San Francisco (for example, Bolt, 1968; Lomax, 2005), with the 

rupture extending northward through the Offshore of Tomales Point map area to the south flank of Cape 

Mendocino (Lawson, 1908; Brown and Wolfe, 1972). 

The Point Reyes Peninsula is bounded to the south and west in the offshore by the north- and 

east-dipping Point Reyes Thrust Fault (McCulloch, 1987; Heck and others, 1990; also see fig. 1 on sheet 

10), which lies about 20 km west of Tomales Point. Granitic basement rocks are offset about 1.4 km on 

this thrust fault offshore of Point Reyes (McCulloch, 1987), and this uplift combined with west-side-up 

offset on the San Andreas Fault (Grove and Niemi, 2005) resulted in uplift of the Point Reyes Peninsula, 

including Tomales Point and the adjacent continental shelf. Grove and others (2010) reported uplift rates 

of as much as 1 mm/yr for the south flank of the Point Reyes Peninsula based on marine terraces, but 

reported no datable terrace surfaces that could constrain uplift for the flight of 4–5 terraces exposed 

farther north along Tomales Point. 

Because of this Quaternary uplift and relative lack of sediment supply from coastal watersheds, 

there is extensive rugged, rocky seafloor beneath the continental shelf in the Offshore of Tomales Point 

map area. Granitic rocks (unit Kg) on the seafloor are mapped on the basis of massive character, 

roughness, extensive fractures, and high backscatter (sheet 3). Neogene sedimentary rocks (units Tl and 
28

Tu) commonly form distinctive “ribs,” created by differential seafloor erosion of dipping beds of 

variable resistance. The more massive offshore outcrops of unit Tu in the southern part of the map area 

are inferred to represent more uniform lithologies. Slopes on the granitic seafloor (generally 1° to 1.3°) 

are greater than those over sedimentary rock (generally about 0.5° to 0.6°). 

Sediment-covered areas occur in gently sloping (less than about 0.6°) midshelf environments 

west and north of Tomales Point, and at the mouth of Tomales Bay. Sediment supply is local, limited to 

erosion from local coastal bluffs and dunes, small coastal watersheds, and sediment flux out of the 

mouth of Tomales Bay. Shelf morphology and evolution largely reflects eustacy; sea level has risen 

about 125 to 130 m over about the last 21,000 years (for example, Lambeck and Chappell, 2001; Peltier 

and Fairbanks, 2006), leading to broadening of the continental shelf, progressive eastward migration of 

the shoreline and wave-cut platform, and associated transgressive erosion and deposition. 

Given present exposure to high wave energy, modern nearshore to midshelf sediments are mostly 

sand (unit Qms) and a mix of sand, gravel, and cobbles (units Qmsc and Qmsd). These sediments are 

distributed between rocky outcrops at water depths of as much as 65 m (see below). Coarser grained 

sands and gravels (units Qmsc and Qmsd) are recognized primarily on the basis of bathymetry and 

high backscatter (sheets 1, 2, 3). 

Unit Qmsd typically is mapped as erosional lags in scour depressions (see, for example, 

Cacchione and others, 1984) that are bounded by relatively sharp contacts with bedrock, or sharp to 

diffuse contacts with units Qms and Qmsc. These depressions typically are a few tens of centimeters 

deep and range in area from a few tens of square meters to more than one square kilometer. Such scour 

depressions are common along this stretch of the California coast (see, for example, Cacchione and 

others, 1984; Hallenbeck and others, 2012; Davis and others, 2013) where offshore sandy sediment can 

be relatively thin (thus unable to fill the depressions) owing to lack of sediment supply from rivers and

also to significant erosion and offshore transport of sediment during large northwest winter swells. Such 

features have been referred to as “rippled-scour depressions” (see, for example, Cacchione and others, 

1984) or “sorted bedforms” (see, for example, Murray and Thieler, 2004; Goff and others, 2005; 

Trembanis and Hume, 2011). Although the general areas in which both unit Qmsd scour depressions 

and surrounding Qms sand sheets are found are not likely to change substantially, the boundaries of the 

unit(s) likely are ephemeral, changing seasonally and during significant storm events. 

Unit Qmsf consists primarily of mud and muddy sand and is commonly extensively bioturbated. 

The location of the inboard contact at water depths of about 65 m is based on meager sediment sampling 

and photographic data (sheets 5, 6) and the inference that it must lie offshore of the outer boundary of 

coarse-grained units Qmsd and Qmsc. This is notably deeper than the inner contact of unit Qmsf

offshore of the nearby Russian River (about 50 m; Klise, 1984), which result from both increased wave 

energy and significantly decreased supply of muddy sediment. 

Two areas of high-backscatter (see sheet 3) and rough seafloor (unit ) are notable in that each 

includes several small (less than about 20,000 m2

), irregular “mounds” that have as much as 1 m of 

positive relief above the surrounding seafloor. West of northern Tomales Point, unit  is mapped in 

water depths of between 65 and 70 m, and the orientation of the individual mounds ranges from 

randomly distributed to northwest-trending. Seismic-reflection data (see, for example, fig. 4 on sheet 8) 

reveal that this lumpy material rests on several meters of uppermost Pleistocene to Holocene sediment 

and, thus, is not bedrock outcrop. We think this material is most likely marine debris, possibly derived 

from the more than 60 shipwrecks that occurred offshore of the Point Reyes peninsula between 1849 and 

1940 (National Park Service, 2012). It also is conceivable that this lumpy terrain consists of biological 

“hardgrounds” (that is, groups of fauna on the seafloor with rigid, often calcareous, shells that exhibit 

high reflectivity, similar to lithified rock). 
29

Units Qsw, Qstb, Qdtb, and Qkdtb comprise sediments in Tomales Bay. Anima and others 

(2008) conducted a high-resolution bathymetric survey of Tomales Bay and noted that strong tidal 

currents at the mouth of the bay had created a large field of sandwaves, dunes, and flats (unit Qsw). Unit 

Qkdtb is a small subaqueous sandy delta deposited at the mouth of Keys Creek, the largest coastal 

watershed draining into this northern part of Tomales Bay. Unit Qstb occurs south of units Qsw and 

Qdtb, and comprises largely flat seafloor underlain by mixed sand and silt. Unit Qdtb consists of 

depressions within the sedimentary fill of Tomales Bay. These depressions commonly occur directly 

offshore of coastal promontories, cover as much as 74,000 m2, and are as deep as 9 m. The relative 

proportions of all offshore map units are shown in table 8–1. 

Table 8–1. Areas and relative proportions of offshore geologic map units in Offshore of Tomales Point map area.

Map Unit Area (m2) Area (km2) Percent of total area

Marine sedimentary units

Qmsr 121,009 0.1 0.1

Qms 39,278,404 39.3 31.4

Qmsc 5,606,064 5.6 4.5

Qmsf 31,709,349 31.7 25.4

Qmsd 7,141,722 7.1 5.7

 Total, sedimentary units 83,856,547 83.9 67.1

Marine bedrock and (or) shallow bedrock units

Tu 18,014,905 18.0 14.4

Tl 382,910 0.4 0.3

Kg 22,804,258 22.8 18.2

 Total, bedrock units 41,202,073 41.2 32.9

 Total, California’s State Waters 125,058,620 125.1 100.0

Tomales Bay units

Qsw 7,077,418 7.1 39.7

Qstb 9,226,965 9.2 51.7

Qkdtb 1,370,212 1.4 7.7

Qdtb 155,368 0.2 0.9

 Total, Tomales Bay map area 17,829,963 17.8 100.0
30

DESCRIPTION OF MAP UNITS

OFFSHORE GEOLOGIC AND GEOMORPHIC UNITS

Qsr Marine shelf deposits, rough seafloor (late Holocene)—Randomly distributed to 

northwest-trending, irregular “mounds” (as large as 20,000 m2) that have as much as 

1 m of positive relief above seafloor; interpreted as marine debris; possibly related to 

either one or more shipwrecks or biological “hardgrounds” 

Qms Marine nearshore and shelf deposits (late Holocene)—Mostly sand; ripple marks 

common; found on gently seaward-dipping (less than 1°) surface between nearshore 

and water depths of about 65 m 

Qmsc Coarse-grained marine nearshore and shelf deposits (late Holocene)—Predominantly 

coarse sand, gravel, and cobbles; found on gently seaward-dipping (less than 1°) 

surface in water depths up to 65 m; recognized primarily on basis of high backscatter 

and flat relief 

Qmsf Fine-grained marine shelf deposits (late Holocene)—Predominantly mud, very fine sand, 

and silt; commonly bioturbated; found on gently seaward-dipping (less than 1°) 

surfaces at depths greater than about 65 m 

Qmsd Marine shelf scour depressions (late Holocene)—Inferred to be coarse sand and possibly 

gravel; consists of irregular, arcuate scour depressions that vary from solitary features 

occupying a few hundred square meters to fields of interconnected depressions 

covering tens of thousands of square meters. Found as single depressions or in fields 

of depressions interspersed with elevated shelf sediments (units Qms and Qmsc). 

Depressions typically are 15 to 50 cm deep, and they have sharp to diffuse 

boundaries. In map area, both backscatter data and direct camera observations show 

small intensity contrasts, suggesting that depressions are filled with sediment that is 

coarser than intervening elevated sandy shelf deposits; general area in which unit is 

found is not likely to change substantially, but boundaries of unit(s) and locations of 

individual depressions (and intervening flat sheets) likely are ephemeral, changing 

during significant storm events 

Qstb Sediments of central Tomales Bay (late Holocene)—Mixed fine sand and silt on the 

mostly flat floor of Tomales Bay. Anima and others (2008) report that sediment in the 

south-central part of the bay is fine sand to coarse silt; they sampled fine to very fine 

sand at the mouths of several small coastal watersheds 

Qsw Sand at the mouth of Tomales Bay (late Holocene)—Anima and others (2008) report that 

coarse to medium sand is present at the mouth of Tomales bay, forming a large field 

of sand waves, dunes, and flats 

Qkdtb Subaqueous delta at the mouth of Walker Creek (late Holocene)—Semicircular 

subaqueous delta extending into Tomales Bay from the mouth of Walker Creek 

Qdtb Seafloor depressions in Tomales Bay (late Holocene)—Oval to oblate depressions within 

the sedimentary fill of Tomales Bay. Individual depressions are as much as 74,000 m2

in area and are as much as 9 m deep

Tu Sedimentary rocks, undivided (late Pliocene to middle Miocene)—Consists of Laird 

Sandstone (unit Tl), Monterey Formation (unit Tm), Santa Margarita Sandstone (unit 

Tsm), and Purisima Formation (unit Tp) (see below); units decrease in age to the 

southwest 
31

Tl Laird Sandstone (middle Miocene)—Marine arkosic sandstone, includes basal granitic 

conglomerate 

Kg Granitic rocks (Cretaceous)—Offshore equivalent of the tonalite of Tomales Point (unit 

Kgd) and the Granodiorite and granite of Inverness Ridge (unit Kgr) (Clark and 

Brabb, 1997); mapped based on high backscatter and rough, massive, fractured, 

seafloor morphology 

ONSHORE GEOLOGIC AND GEOMORPHIC UNITS

[Units are compiled from Clark and Brabb (1997), Witter and others (2006), and Wagner and Gutierrez 

(2010)] 

af Artificial fill (late Holocene)—Material placed by humans

afem Artificial fill over estuarine mud (late Holocene)—Material deposited by humans over 

estuarine sediments 

alf Artificial levee fill (late Holocene)— Constructed levees bordering rivers, streams, sloughs 

and islands for the purpose of containing flood or tidal waters 

adf Artificial-dam fill (late Holocene)—Earth- or rock-fill dams, embankments and levees; 

constructed to impound land-locked water bodies 

Qsc Stream channel deposits (late Holocene)—Fluvial deposits within active, natural stream 

channels

Qbs Beach-sand deposits (late Holocene)—Active beaches in coastal environment; may form 

veneer over bedrock platform 

Qt Stream terrace deposits (late Holocene)—Stream terrace deposits judged to be late 

Holocene (<1,000 years) in age based on records of historical inundation and (or) 

identification of youthful meander scars and braided bars on aerial photographs or 

lidar images

Qot Stream terrace deposits (Holocene)—Stream terrace sediments deposited in point bar and 

overbank environments 

Qds Dune sand (Holocene)—Active dunes and recently stabilized dunes in coastal environments 

Qe Estuarine deposits (Holocene)—Heterogeneous mixture of coarse and fine estuarine 

sediment; deposited in Drakes Estero (southern edge of map) and at Toms Point on 

the east shore of Tomales Bay

Qed Estuarine-delta deposits (Holocene)—Heterogeneous mixture of coarse and fine estuarine 

sediment; deposited in delta at mouths of tidally influenced coastal streams, where 

fresh water mixes with seawater

Qa Alluvial deposits, undivided (Holocene)—Alluvium deposited in fan, terrace, or basin 

environments 

Qf Alluvial fan deposits (Holocene)—Sediment deposited by streams emanating from 

mountain canyons onto alluvial valley floors or alluvial plains; may include debris 

flow, hyper-concentrated mudflow, and braided stream deposits 

Qof Alluvial fan deposits, undivided (Holocene and late Pleistocene)—Mapped in small 

valleys where separate fan, basin, and terrace units could not be delineated at map

scale, and where deposits might be of either late Pleistocene or Holocene age 

Qc Colluvium (Holocene and late Pleistocene)—Unsorted clay, silt, sand, gravel, and rock 

debris, in varying proportions 

Qls Landslide deposits (Holocene and Pleistocene)—Weathered and disintegrated rocks and 
32

soil, physically weathered, mapped units range from deep-seated landslides to active 

colluvium 

Qods Older dune sand (late Pleistocene(?))—Dunes stabilized by vegetation; forms large 

complex east of the mouth of Tomales Bay 

Qml Millerton Formation (late Pleistocene)—Alluvial and estuarine clay, silt, sand and gravel 

deposited on terraces along the eastern margin of Tomales Bay

Qmt Marine terrace deposits (late Pleistocene)—Marine sediments uplifted to form terraces 

along the east coast of Tomales Bay and on the southeast coast of Bodega Bay 

Qobs Beach sand in uplifted marine terraces (late Pleistocene(?))—Reddish-brown, friable sand 

and fine gravel; occur along the west coast of Tomales Point, north of Abbots Lagoon 

Tp Purisima Formation (late Pliocene to late Miocene)—Marine siltstone, sandstone, and 

mudstone; locally contains diatomite

Twg Wilson Grove Formation (Pliocene and late Miocene)—Marine sandstone and 

conglomerate, occurs in northeast corner of map area, east of Tomales Bay and 

Bodega Bay

Tsm Santa Margarita Sandstone (late Miocene)—Massive marine glauconitic and bituminous 

arkosic sandstone 

Tm Monterey Formation (late and middle Miocene)—Marine, thin-bedded chert, porcelanite, 

shale, and sandstone 

Tl Laird Sandstone (middle Miocene)—Marine arkosic sandstone that contains basal graniticboulder conglomerate

Kgr Granodiorite and granite of Inverness Ridge (Late Cretaceous)—Grandiorite and granite; 

aplite and alaskite dikes and masses are locally abundant

Kgd Tonalite of Tomales Point (Late Cretaceous)—Hornblende-biotite tonalite that contains 

dark diorite inclusions 

Franciscan complex 

KJfss Sandstone and shale in Nicasio Reservoir terrane (Cretaceous and Jurassic) 

KJfgs Greenstone in Central belt (Cretaceous and Jurassic) 

fsr Mélange in Central belt (Cretaceous and Jurassic)—Sheared argillite, graywacke, and 

minor green tuff matrix enclosing blocks and lenses of sandstone, shale, chert, 

metachert, and serpentinite 

ss Sandstone and shale blocks within mélange

ch Chert and metachert blocks within mélange

sp Serpentinized ultramafic rocks within mélange

 Metamorphic rocks (Age uncertain, probably Mesozoic or Paleozoic)—Intruded by 

Cretaceous granitic rocks; includes mica schist, quartzite, calc-hornfels, and marble 

(Clark and Brabb, 1997); occurs on east shore of Tomales Point 
33

Acknowledgments

This publication was funded by the California Ocean Protection Council and the U.S. Geological 

Survey (USGS) Coastal and Marine Geology Program. We thank the officers, crew, and scientific 

parties of the ships—R/V VenTresca, California State University, Monterey Bay, Seafloor Mapping 

Lab; F/V Quicksilver, Fugro Pelagos; and R/V Frontier, U.S. Geological Survey—for their skill and 

professionalism in collecting the data presented in this report. We thank Robert Garrison, Stephen Watt, 

and Scott Starratt (all USGS) for their critical reviews that greatly improved this report. We are very 

grateful to USGS editor Taryn Lindquist for helping us develop the templates and formats for this series 

of publications, and for invaluable editorial review and suggestions. 
34

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