California State Waters Map Series—Offshore of Half 

Moon Bay, California

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

Bryan E. Dieter, Michael W. Manson, Ray W. Sliter, Stephanie L. Ross, Janet T. Watt, Charles A. Endris, Rikk G. 

Kvitek, Eleyne L. Phillips, Mercedes D. Erdey, John L. Chin, and Carrie K. Bretz 

(Guy R. Cochrane and Susan A. Cochran, editors)

Pamphlet to accompany

Open-File Report 2014–1214

2014

U.S. Department of the Interior

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

SALLY JEWELL, Secretary 

U.S. Geological Survey 

Suzette Kimball, Acting Director 

U.S. Geological Survey, Reston, Virginia: 2014 

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

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

Suggested citation:

Cochrane, G.R., Dartnell, P., Greene, H.G., Johnson, S.Y., Golden, N.E., Hartwell, S.R., Dieter, B.E., Manson, 

M.W., Sliter, R.W., Ross, S.L., Watt, J.T., Endris, C.A., Kvitek, R.G., Phillips, E.L., Erdey, M.D., Chin, J.L., and 

Bretz, C.K. (G.R. Cochrane and S.A. Cochran, eds.), 2014, California State Waters Map Series—Offshore of Half 

Moon Bay, California: U.S. Geological Survey Open-File Report 2014–1214, pamphlet 37 p., 10 sheets, scale 

1:24,000, http://dx.doi.org/10.3133/ofr20141214. 

ISSN 2331-1258 (online)

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

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

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

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

By Guy R. Cochrane

Regional Setting .........................................................................................................................................................3

Publication Summary..................................................................................................................................................4

Chapter 2. Bathymetry and Backscatter-Intensity Maps of the Offshore of Half Moon Bay Map Area (Sheets 1, 2, 

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

By Peter Dartnell, Rikk G. Kvitek, and Carrie K. Bretz

Chapter 3. Data Integration and Visualization for the Offshore of Half Moon Bay Map Area (Sheet 4)........................10

By Peter Dartnell

Chapter 4. Seafloor-Character Map of the Offshore of Half Moon Bay Map Area (Sheet 5) ........................................11

By Guy R. Cochrane, Eleyne L. Phillips, and Mercedes D. Erdey

Chapter 5. Ground-Truth Studies for the Offshore of Half Moon Bay Map Area (Sheet 6)...........................................16

By Nadine E. Golden and Guy R. Cochrane

Chapter 6. Potential Marine Benthic Habitats of the Offshore of Half Moon Bay Map Area (Sheet 7)..........................19

By H. Gary Greene and Charles A. Endris

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 Half Moon Bay Map Area and the Bolinas to 

Pescadero Region (Sheets 8 and 9) ............................................................................................................................22

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

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

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

Seismic-Reflection Imaging of the Continental Shelf................................................................................................24

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

Chapter 8. Geologic and Geomorphic Map of the Offshore of Half Moon Bay Map Area (Sheet 10)...........................27

By H. Gary Greene, Michael W. Manson, Charles A. Endris, and Samuel Y. Johnson

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

Description of Map Units ..........................................................................................................................................29

Offshore Geologic and Geomorphic Units ............................................................................................................29

Onshore Geologic and Geomorphic Units ............................................................................................................30

Acknowledgments........................................................................................................................................................32

References Cited .........................................................................................................................................................33

Figures

Figure 1–1. Physiography of Bolinas to Pescadero region and its environs .................................................................. 6

Figure 1–2. Coastal geography of Offshore of Half Moon Bay 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 Half Moon Bay 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 Half Moon Bay map area.................. 14

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

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

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

Pescadero region, as well as in Offshore of Half Moon Bay map area..................................................... 26

Table 8–1. Areas and relative proportions of offshore geologic map units in Offshore of Half Moon Bay map 

area. ......................................................................................................................................................... 28

Map Sheets

Sheet 1. Colored Shaded-Relief Bathymetry, Offshore of Half Moon Bay Map Area, California

By Carrie K. Bretz, Rikk G. Kvitek, Peter Dartnell, and Eleyne L. Phillips 

Sheet 2. Shaded-Relief Bathymetry, Offshore of Half Moon Bay Map Area, California

By Carrie K. Bretz, Rikk G. Kvitek, Peter Dartnell, and Eleyne L. Phillips

Sheet 3. Acoustic Backscatter, Offshore of Half Moon Bay Map Area, California

By Carrie K. Bretz, Rikk G. Kvitek, Peter Dartnell, and Eleyne L. Phillips

Sheet 4. Data Integration and Visualization, Offshore of Half Moon Bay Map Area, California

By Peter Dartnell

Sheet 5. Seafloor Character, Offshore of Half Moon Bay Map Area, California

By Eleyne L. Phillips, Mercedes D. Erdey, and Guy R. Cochrane

Sheet 6. Ground-Truth Studies, Offshore of Half Moon Bay Map Area, California

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

Sheet 7. Potential Marine Benthic Habitats, Offshore of Half Moon Bay Map Area, California

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

Sheet 8. Seismic-Reflection Profiles, Offshore of Half Moon Bay Map Area, California

By Ray W. Sliter, Samuel Y. Johnson, Stephanie L. Ross, and John L. Chin

Sheet 9. Local (Offshore of Half Moon Bay Map Area) and Regional (Offshore from Bolinas to Pescadero) 

Shallow-Subsurface Geology and Structure, California

By Samuel Y. Johnson, Stephen R. Hartwell, Ray W. Sliter, Janet T. Watt, Eleyne L. Phillips, 

Stephanie L. Ross, Holly F. Ryan, and John L. Chin

Sheet 10. Offshore and Onshore Geology and Geomorphology, Offshore of Half Moon Bay Map Area, California

By H. Gary Greene, Michael W. Manson, Bryan E. Dieter, Stephanie L. Ross, Stephen R. Hartwell, 

and Samuel Y. Johnson
1

California State Waters Map Series—Offshore of Half 

Moon Bay, California

By Guy R. Cochrane,1 Peter Dartnell,1 H. Gary Greene,2 Samuel Y. Johnson,1 Nadine E. Golden,1 Stephen R. 

Hartwell,1 Bryan E. Dieter,2 Michael W. Manson,3 Ray W. Sliter,1 Stephanie L. Ross,1 Janet T. Watt,1 Charles A. 

Endris,2 Rikk G. Kvitek,4 Eleyne L. Phillips,1 Mercedes D. Erdey,1 John L. Chin,1 and Carrie K. Bretz4 

(Guy R. Cochrane1 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 Game, 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. 

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 ESRI5 ArcGIS 

 

1 U.S. Geological Survey

2 Moss Landing Marine Laboratories, Center for Habitat Studies 3 California Geological Survey

4 California State University, Monterey Bay, Seafloor Mapping Lab

5 Environmental Systems Research Institute, Inc.
2

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 June 10, 2013). 

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 Game, 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. 
3

Chapter 1. Introduction

By Guy R. Cochrane

Regional Setting

The map area offshore of the city of Half Moon Bay, California, which is referred to herein as 

the “Offshore of Half Moon Bay” map area (figs. 1–1, 1–2) is located in northern California, on the 

Pacific Coast of the San Francisco Peninsula about 40 kilometers south of the Golden Gate. The city of 

Half Moon Bay (population, about 11,000) is the nearest significant onshore cultural center (fig. 1–1). 

The Pillar Point Harbor at the north edge of Half Moon Bay offers a protected landing for boats and 

provides other marine infrastructure. The harbor, which was formed by the construction of two riprap 

jetties, is managed by the San Mateo County Harbor District. The harbor has 369 berthing slips and 

supports a commercial fishing fleet and search-and-rescue services.

The Offshore of Half Moon Bay map area lies offshore of the Santa Cruz Mountains (fig. 1–1), 

part of the northwest-trending Coast Ranges that run roughly parallel to the San Andreas Fault Zone 

(California Geological Survey, 2002a). The western margin of North America is the only continental 

margin in the world delineated largely by transform faults such as the San Andreas Fault (Dickinson, 

2004). The Santa Cruz Mountains lie between the San Andreas Fault Zone and the San Gregorio Fault 

system.

Such faults have played an important role in the development of the map area. The flat coastal 

area (the most recent of numerous marine terraces) was formed by wave erosion about 105 thousand 

years ago (Weber, 1990). The higher elevation of this same terrace west of the Half Moon Bay airport is

caused by uplift on the Seal Cove Fault, a splay of the San Gregorio Fault Zone (see sheet 10). Although 

originally incised into the rising terrain horizontally, the ancient terrace surface has been gently folded 

into a northwest-plunging syncline by compression related to right-lateral strike-slip movement along 

the San Gregorio Fault Zone (Weber, 1990). The lowest elevation coincides with the deepest part of the 

embayment at Half Moon Bay; the terrace surface rises both to the north and to the south (Lajoie, 1986). 

A westward bend in the San Andreas Fault Zone, coupled with right-lateral movement along the 

Seal Cove Fault (Weber, 1990), which comes ashore in Pillar Point Harbor (Dickinson and others, 

2005), has resulted in the folding and uplifting of sedimentary rocks of the Purisima Formation in the 

offshore, forming the folds and faults that are visible on the seafloor from the headland at Pillar Point 

(see sheet 10). Differential erosion of the folded layers of the Purisima Formation has exposed the 

parallel curved-rock ridges that are visible on the seafloor and in the bathymetry data (see sheets 1, 2). 

Exposures of granitic rocks of the Salinian block are found in the Moss Beach area north of 

Pillar Point, east of the San Gregorio Fault (see sheet 10). In the Bolinas to Pescadero region, Salinian 

block granitic rocks lie between the San Gregorio Fault system and the San Andreas Fault Zone, and 

they likely are part of a block that has been transported approximately 155 km north from the south end 

of the Sierra Nevada batholith by motion along the San Andreas transform fault system (Dickinson and 

others, 2005). 

Uplift in this map area has resulted in relatively shallow water depths within California’s State 

Waters (0 to 55 m) and, thus, little accommodation space for sediment accumulation. Sediment is 

observed in the shelter of Half Moon Bay and on the outer half of the California’s State Waters shelf. 

Sediment in the area is mobile, often forming dunes and sand waves. 

The Offshore of Half Moon Bay map area lies near the midpoint of the San Francisco littoral cell 

(Hapke and others, 2006), which is characterized by north-to-south littoral transport of sediment that is 

derived mainly from San Francisco Bay, ephemeral streams, and local coastal erosion. Offshore beyond 

California’s State Waters, unnamed canyons that incise the slope have been disconnected from coastal 
4

streams by the rising sea level, which has risen about 125 m since the lowstand associated with the Last 

Glacial Maximum, about 18,000 to 20,000 years ago (Fairbanks, 1989; Fleming and others, 1998; 

Lambeck and Chappell, 2001; Lambeck and others, 2002). In the map area, no major submarine canyons 

extend beyond the shelf break up into the nearshore to receive littoral drift. 

Griggs and others (2005) categorized erosion of the coastline in the map area as either moderate 

or high risk as opposed to stable low risk. From north to south, types of erosion include (1) cliff erosion 

from wave attack along the exposed northern coast, (2) erosion at the east end and south of the harbor 

breakwater owing to the refraction of wave energy by the breakwater, and (3) erosion around armored 

shoreline in the Miramar Beach area (fig. 1–1).

The benthic species observed in the Offshore of Half Moon Bay map area are natives of the coldtemperate biogeographic zone named either the “Oregonian province” (Briggs, 1974) or the “northern 

California ecoregion” (Spalding and others, 2007). This biogeographic province is maintained by the 

long-term stability of the southward-flowing California Current, an eastern limb of the North Pacific 

subtropical gyre that flows from Oregon to Baja California. At its midpoint off central California, the 

California Current transports subarctic surface (0–500 m deep) waters southward, about 150 to 1,300 km 

from shore (Lynn and Simpson, 1987; Collins and others, 2000). Seasonal northwesterly winds (Inman 

and Jenkins, 1999) that are, in part, responsible for the California Current, generate coastal upwelling. 

The south end of the Oregonian province is at Point Conception (about 365 km south of the map area), 

although its associated phylogeographic group of marine fauna may extend beyond to the area offshore 

of Los Angeles in southern California (Dawson and others, 2006). The ocean off central California has 

seen a warming over the last 50 years that is driving an ecosystem shift from the productive subarctic 

regime towards a depopulated subtropical environment (McGowan and others, 1998). 

 The Offshore of Half Moon Bay map area lies within the Shelf (continental shelf) megahabitat 

of Greene and others (1999). Habitats range from significant rocky outcrops that support kelp-forest 

communities nearshore to rocky-reef communities in deep water. Biological productivity resulting from 

coastal upwelling supports populations of Sooty Shearwater (Puffinus griseus), Western Gull (Larus 

occidentalis), Common Murre (Uria aalge), Cassin’s Auklet (Ptychoramphus aleuticus), and many 

other less populous bird species (Ainley and Hyrenbach, 2010). In addition, an observable recovery of 

Humpback and Blue Whales (Megaptera novaeangliae and Balaenoptera musculus, respectively) has 

occurred in the area; both species are dependent on coastal upwelling to provide nutrients (Calambokidis 

and Barlow, 2004). The large extent of exposed inner shelf bedrock supports large forests of “bull kelp” 

(Nereocystis luetkeana) (Miller and Estes, 1989), which is well adapted for high wave-energy 

environments (Koehl and Wainwright, 1977). Common fish species found in the kelp beds and rocky 

reefs include blue rockfish (Sebastes mystinus), black rockfish (Sebastes melanops), olive rockfish 

(Sebastes serranoides), kelp rockfish (Sebastes atrovirens), gopher rockfish (Sebastes carnatus), blackand-yellow rockfish (Sebastes chrysomelas), painted greenling (Oxylebius pictus), kelp greenling 

(Hexagrammos decagrammus), and lingcod (Ophiodon elongatus) (Stephens and others, 2006). 

Wind directions along the northern California coast typically are from the west-northwest; 

however, during the winter, strong North Pacific storms generate large, long-period waves from more 

westerly directions that shoal and break over the bedrock reef offshore of Pillar Point Harbor at the 

world-famous surfing location known as Mavericks. Waves can routinely crest at over 7.5 m during 

these conditions and may reach 24 m. 

Publication Summary

This publication about the Offshore of Half Moon Bay 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 
5

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 flat, sediment-covered inner continental to midcontinental shelf, as well as shallow “scour 

depressions” and local, tectonically controlled bedrock uplifts. 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 Bolinas to Pescadero region, interpreted on the basis of the seismic-reflection data. 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), and high-resolution seismic-reflection profiles 

(sheet 8).

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 Bolinas to Pescadero region and its environs. Box shows Offshore of Half Moon Bay 

map area. Yellow line shows limit of California’s State Waters. Dashed white line shows trace of San Andreas 

Fault Zone (SAFZ). Other abbreviations: GG, Golden Gate; HMB, Half Moon Bay; SCM, Santa Cruz Mountains; 

SFP, San Francisco Peninsula; SG, San Gregorio; SM, San Mateo.
7

Figure 1–2. Coastal geography of Offshore of Half Moon Bay map area. Yellow line shows limit of California’s 

State Waters. Dashed white line shows trace of San Gregorio Fault Zone (SGFZ). Other abbreviations: HBA, 

Half Moon Bay Airport; HMB, city of Half Moon Bay; MAB, Martins Beach; MOB, Moss Beach; MI, Miramar 

Beach; MV, Mavericks; PM, Point Montara; PP, Pillar Point; PPH, Pillar Point Harbor.
8

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

of Half Moon Bay Map Area (Sheets 1, 2, and 3)

By Peter Dartnell, Rikk G. Kvitek, and Carrie K. Bretz

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

acoustic-backscatter (sheet 3) maps of the Offshore of Half Moon Bay map area in northern California 

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

State University, Monterey Bay (CSUMB) (fig. 1 on sheets 1, 2, 3). The nearshore area was mapped by 

CSUMB in 2007; the areas further offshore, by Fugro Pelagos in 2006 and 2007. Both used a 

combination of 400-kHz Reson 7125 and 244-kHz Reson 8101 multibeam echosounders. 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 all the 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 realtime 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. Backscatter 

data were postprocessed using Geocoder version 3.2 (Fugro Pelagos modified test release 16). Within 

Geocoder, the backscatter intensities were radiometrically corrected (including despeckling and anglevarying 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 into a 1-mresolution image. 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 anti-aliasing 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.

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 blueish greens to represent greater depths (note that the Offshore of Half Moon Bay 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). 

Bathymetric contours (sheets 1, 2, 3, 5, 7, 10) were generated at 10-m intervals from the merged 

2-m-resolution bathymetric surface. 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. 
9

The backscatter grids were combined in a GIS to create an acoustic-backscatter map (sheet 3), on 

which 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 1-m-resolution topographic-lidar data collected by Photoscience in 

2005 for the U.S. Geological Survey and the County of San Mateo.
10

Chapter 3. Data Integration and Visualization for the Offshore of Half 

Moon Bay 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. These data are used by researchers to develop maps, reports, and other tools to assist in the 

coastal and marine spatial-planning capability of coastal-zone managers and other stakeholders. For 

example, seafloor-character (sheet 5), habitat (sheet 7), and geologic (sheet 10) maps of the Offshore of 

Half Moon Bay 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 three-dimensional representations such as those displayed on the data integration 

and visualization sheet for the Offshore of Half Moon Bay 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 light blues 

represent deeper depths. Digital orthophotographs were draped over the topography data, and the 

acoustic-backscatter geoTIFF images were 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, 2, 4, 5, 6, and 7 on sheet 4. These views highlight the seafloor morphology in 

the Offshore of Half Moon Bay map area, which includes exposed outcrops of fractured bedrock and 

complex patterns of shallow depressions. 

Video-mosaic images created from digital seafloor video (for example, fig. 3 on sheet 4) display 

the geologic complexity (rock, sand, and mud; see sheet 10) and biologic complexity 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 over the seafloor, at 

speeds 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 with seismic-reflection-profile data help integrate 

surface and subsurface observations, especially stratigraphic and structural relations (for example, fig. 7 

on sheet 4). These block diagrams were created by converting digital seismic-reflection-profile 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 Half Moon Bay 

Map Area (Sheet 5)

By Guy R. Cochrane, Eleyne L. Phillips, and Mercedes D. Erdey

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 Game (CDFG), has identified seven substrate-defined 

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 Game, 2008). The CDFG 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 CDFG 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 Half Moon Bay 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 San Gregorio 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, which is a standard calculation 

performed with the National Oceanic and Atmospheric Administration (NOAA) benthic-terrain modeler 

(available at http://www.csc.noaa.gov/digitalcoast/tools/btm/index.html; last accessed April 5, 2011), 

using a 3-pixel by 3-pixel array of bathymetry. 

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 datacollection 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), 

Depth Zone 4 (100 to 200 m), and Depth Zone 5 (greater than 200 m); in the Offshore of Half Moon 
12

Bay 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 of Half Moon Bay map area, only Slope Class 1 is 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 (71.6 km2

) of the map area: 15.1 

percent (19.2 km2) is in Depth Zone 2, and 41.4 percent (52.4 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 16.2 percent (20.5 km2) of the map area: 8.5 percent (10.8 

km2) is in Depth Zone 2, and 7.7 percent (9.7 km2) is in Depth Zone 3. Rock and boulder, rugose (rock 

outcrops and boulder fields having high surficial complexity) makes up 22.6 percent (28.6 km2

) of the 

map area: 18.9 percent (24.0 km2) is in Depth Zone 2, and 3.6 percent (4.6 km2) is in Depth Zone 3. 

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

surrounding seafloor) makes up 4.8 percent (6.0 km2) of the map area: 0.6 percent (0.8 km2) is in Depth 

Zone 2, and 4.1 percent (5.2 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 

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

the observed sediment type at a certain location. 
13

The seafloor in the Offshore of Half Moon Bay map area has extensive areas of Class III habitat 

composed of layered sedimentary rocks uplifted and folded by regional faulting. A sufficient number of 

video observations were made to complete accuracy assessment for all four sediment classes. 

The classification accuracy of Classes I, III, and IV (67 percent, 61 percent, and 92 percent 

accurate, respectively; table 4–2) is determined by comparing the shipboard video observations and the 

classified map. The weaker (44 percent accurate) agreement in Class II (mixed smooth sediment and 

rock and flat rock outcrop) likely is due to the relatively narrow and intermittent nature of transition 

zones from sediment to rock and also the size of the buffer; a strong likelihood exists for a Class II 

(mixed) pixel to be interspersed with pixels belonging to other classes. A single buffered observation 

locale of 78 pixels, therefore, is likely to be interspersed with other classes of pixels in addition to Class 

II. 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 (90 percent for Class I, 94 percent for Class II, 95 percent for Class III, and 90 

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 Half Moon Bay 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

sand mud low

sand mud trace

sand sand low

sand sand moderate

sand sand trace

sand shell hash low

sand shell hash moderate

shell hash sand moderate

Class II

boulders cobbles low

boulders sand low

cobbles boulders low

cobbles cobbles low

cobbles cobbles moderate

cobbles gravel low

cobbles mud moderate

cobbles rock low

cobbles sand low

cobbles sand moderate

cobbles shell hash low

gravel gravel low

gravel sand low

gravel shell hash low

mud cobbles low

mud rock low

rock boulders low

rock cobbles low

rock mud low

rock rock low

rock sand low

rock sand trace

sand boulders low

sand boulders moderate

sand cobbles low

sand cobbles moderate

sand gravel low

sand gravel moderate

sand rock low

sand rock moderate

shell hash gravel moderate
15

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 Half Moon Bay map area.—Continued

[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 III

boulders boulders high

boulders boulders moderate

boulders cobbles moderate

boulders rock moderate

boulders sand high

boulders sand moderate

cobbles boulders moderate

cobbles rock moderate

mud rock moderate

rock boulders high

rock boulders moderate

rock cobbles high

rock cobbles moderate

rock mud moderate

rock rock high

rock rock moderate

rock sand high

rock sand moderate

sand rock high

Class IV

sand sand moderate

sand shell hash moderate

shell hash sand moderate

megaripples

oscillatory megaripples

depression

Table 4–2. Accuracy-assessment statistics for seafloor-character-map classifications in Offshore of Half Moon Bay 

map area.

[Accuracy assessments are based on video observations (N/A, no accuracy assessment was conducted)]

Class Number of observations % majority % presence/absence

I—Fine- to medium grained smooth sediment 335 67.0 90.5

II—Mixed smooth sediment and rock 328 43.7 94.2

III—Rock and boulder, rugose 392 61.3 94.9

IV—Medium- to coarse-grained sediment (in 

scour depressions) 31 91.6 90.3
16

Chapter 5. Ground-Truth Studies for the Offshore of Half Moon Bay 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 Half Moon Bay map area to collect video and photographic data 

that would “ground truth” the seafloor. This ground-truth surveying occurred on two separate cruises in 

2007 and 2008. The camera sled was towed 1 to 2 m over the seafloor at speeds of between 1 and 2 

nautical miles/hour. Ground-truth surveys in this map area include approximately 18.39 trackline 

kilometers of video and 479 still photographs, in addition to 545 recorded seafloor observations of 

abiotic and biotic attributes. A visual estimate of slope also was recorded.

During the 2007 cruise, the USGS camera sled housed two standard-definition (640×480 pixel 

resolution) video cameras: one was forward looking, and the other was downward looking. During the 

2008 cruise, a larger camera sled was used that housed two standard-definition (640×480 pixel 

resolution) video cameras (one forward looking and one downward looking), as well as 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 

Figure 5–1. Photograph of camera sled used in USGS 2008 ground-truth survey.
17

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

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 D); 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 the Offshore 

of Half Moon Bay map area contains extensive areas of rocky habitat, mostly in the form of folded and 

differentially eroded sedimentary bedrock. Low areas formed where rock is more easily eroded; these 

areas often are covered with coarse sediment. Habitat grades into sand-dominated sediment that has 

bedforms indicative of bottom-current transport.
18

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

Offshore of Half Moon Bay map area.
19

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

Moon Bay Map Area (Sheet 7)

By H. Gary Greene and Charles A. Endris

The map on sheet 7 shows “potential” marine benthic habitats in the Offshore of Half Moon Bay 

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 Half Moon Bay 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 Half Moon Bay 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 

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

Seafloor Slope, Seafloor Complexity, and Geologic Unit. Additional categories of Macro/Microhabitat, 
20

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 Half Moon Bay 

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)/p = Pinnacle indistinguishable from boulder 

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

e = Exposure; bedrock 

g = Gully; channel

h = Hole; depression

m = Mound; linear ridge 

p = Pinnacle; cone 

s = Scarp, cliff, fault, or slump scar 

w = Dynamic bedform

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 a hyphen or in 

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

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

_a-dd = Dredge disturbance

_a-dg = Dredge groove or channel

_a-dm = Dredge mound (disposal) 

_a-dp = Dredge pothole 

_a-f = Ferry (or other vessel) propeller-wash scour or scar 

_a-g = Groin, jetty, rip-rap

_a-p = Pipeline

_a-td = Trawl disturbance 
21

_b = Bimodal (conglomeratic, mixed [gravel, cobbles, and pebbles])

_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 = Rippled 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 Half Moon Bay map area are 11 potential marine benthic habitat 

types, all located on the continental shelf (“Shelf” megahabitat), with two anthropogenic habitats found 

near the Pillar Point Harbor entrance. The meso- and macrohabitats include deformed sedimentaryoutcrops, flat hard rock exposures, and rugose and fractured granitic rock, as well as dynamic features 

such as mobile sand sheets and associated scour depressions. 

Most of the Offshore of Half Moon Bay map area is located on the relatively flat and eroded 

continental shelf. Backscatter data show that the map area is dominated by “soft” sediment; however, 

the highly deformed and differentially eroded bedrock outcrops and their seafloor relief present the most 

spectacular backscatter imagery in this map area. These differentially eroded bedrock areas form the 

local relief and rugosity that make promising potential habitats for rockfish (Sebastes spp.). Sediment 

transport is primarily to the southeast, and sedimentary processes, which are quite active in the map 

area, produce the dynamic bedforms that may be habitats for forage fish such as Pacific sand lance 

(Ammodytes hexapterus). In addition, erosion through shelf sediments down to a coarser lag has 

produced sediment-filled scour depressions that resemble “ripple-scour depressions” of Cacchione and 

others (1984) and Phillips and others (2007), found mainly on the shelf in the northwestern and central 

parts of the map area.

Of the 126.8 km2

 in the map area, 56.25 km2 (44.4 percent) is exposed hard bedrock, and 7.73 

km2 (6.1 percent) consists of sediment-covered bedrock, which is of the mixed hard-soft induration 

class. Soft, unconsolidated sediment covers a total of 70.5 km2

 (55.6 percent), and 62.77 km2 (49.5 

percent) consists of mobile sand sheets, ripple scour depressions, and gravels. Anthropogenic habitats 

cover 0.05 km2 (0.04 percent) and are located in the vicinity of Pillar Point Harbor. 
22

Chapter 7. Subsurface Geology and Structure of the Offshore of Half 

Moon Bay Map Area and the Bolinas to Pescadero Region (Sheets 8 

and 9) 

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

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 Half Moon Bay map area. These data, which are collected at several 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 were collected in 2007 on USGS cruise F–2–07–NC. Singlechannel seismic-reflection data were acquired using two different sources, the SIG 2Mille minisparker 

(figs. 1, 2, 4, 6, 9, 10) and the EdgeTech 512 chirp (fig. 7). The SIG minisparker system 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). The EdgeTech 512 chirp subbottom-profiling 

system consists of a source transducer and an array of receiving hydrophones housed in a 500-lb fish 

towed at a depth of several meters below the sea surface. The swept-frequency chirp source signal was 

500 to 4,500 Hz and 50 ms in length, and it was recorded by hydrophones located on the bottom of the 

fish. 

Figure 3 on sheet 8 shows a seismic-reflection profile collected in 1997 on USGS cruise J–1–97–

MB, using a 0.40- to 5-kHz Geopulse system. Power was supplied by a double-plate, 910-J sound source 

fired at 0.5-second intervals. As with the minisparker and chirp systems, data were digitally recorded 

and merged with GPS navigation data. 

Data for figure 5 on sheet 8 were collected in 1995 on USGS cruise G–2–95–SF (Childs and 

others, 2000; Bruns and others, 2002). Two 0.65-L air guns fired at 12.5-m intervals provided the 

seismic source, and data were digitally recorded on a 24-channel, 150-m-long streamer merged with 

GPS navigation data. Data-processing steps included deconvolution, automatic gain control, filtering at 

50 to 160 Hz, stacking, and migration. 

Figure 8 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 
23

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

a frontier for oil and gas exploration. Much 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 with 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. 

Geologic Structure and Recent Deformation

The Offshore of Half Moon Bay map area straddles the right-lateral San Gregorio Fault system, 

an important structure in the distributed transform boundary between the North American and Pacific 

plates (see, for example, Dickinson and others, 2005). Regionally, this fault is part of a system that is 

present predominantly in the offshore for about 400 km from Point Conception in the south (where it is 

known as the Hosgri Fault) to Bolinas and Point Reyes in the north, extending onland at coastal 

promontories such as Pillar Point in this map area and also at Pescadero Point, 13 km south of the map 

area (see sheet 9; see also, Weber and Lajoie, 1980; Brabb and others, 1998). Offshore parts of this fault 

system are identified on seismic-reflection data 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. 

In the Offshore of Half Moon Bay map area, the San Gregorio Fault forms a distributed, 2- to 5-

km-wide shear zone that narrows northward and includes two main fault strands (see sheets 9, 10). The 

nearshore east strand (also known as the “Seal Cove Fault” or “Coastways Fault;” see figs. 3, 5 on sheet 

8) forms a prominent bathymetric scarp (see sheets 1, 2). Weber (1990), Weber and others (1995), and 

Simpson and others (1997) suggested a dextral slip rate of 3.5 to 4.5 mm/yr for the onland part of the 

east strand on the basis of displacement of onshore marine-terrace shoreline angles and offset alluvial 

fan paleochannels. This estimated rate represents a represents a minimum for the San Gregorio Fault 

system because the offshore west strand (also known as the “Frijoles Fault”; see figs. 1, 2, 3, 4, 5, 6, 7, 

8, 10 on sheet 8) also is active. Cumulative lateral slip on this fault zone is thought to range from 4 to 10 

mm/yr in this area (U.S. Geological Survey and California Geological Survey, 2010). 

The Offshore of Half Moon Bay map area also notably lies along southwestern flank of the 

young, high topography of the Santa Cruz Mountains and Coast Ranges (Maps C, D, E on sheet 9). This 

regional uplift has been linked to a northwest-transpressional bend in the San Andreas Fault (see, for 

example, Zoback and others, 1999). Rates of uplift of marine terraces in and near the map area of as 

much as 0.44 mm/yr confirm that this regional uplift includes the coastal zone (Weber and others, 1995). 

Map E 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) 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 Offshore of Half Moon Bay map area is notably devoid of 

seismicity during this time period. The largest number of earthquakes in the region clearly occur within 

the broad San Andreas Fault Zone between Pacifica and Bolinas; events west of the east strand of the 

San Gregorio Fault and east of the Golden Gate Fault are much less common. Map E also shows the 

inferred location of 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). 
24

Seismic-Reflection Imaging of the Continental Shelf 

Sheet 8 shows seismic-reflection profiles in the Offshore of Half Moon Bay map area, herein 

considered part of the Pacifica-Pescadero shelf. This shelf (see Maps A, B on sheet 9), which is 

relatively flat (less than 0.6°) and shallow (55 m or less), is variably underlain by uppermost Pleistocene 

and Holocene sediment deposited in the last about 21,000 years during the sea-level rise that followed 

the Last Glacial Maximum (LGM) and the last major lowstand. Sea level was about 125 m lower during 

the LGM, at which time the Offshore of Half Moon Bay map area was emergent and the shoreline was 

more than 45 km west of San Francisco, near the Farallon Islands. 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 (Fairbanks, 1989; Fleming and others, 1998; Lambeck and Chappell, 

2001; Peltier and Fairbanks, 2006; Gornitz, 2009). 

The sediments deposited during this latest Pleistocene and Holocene sea-level rise are shaded 

blue in the seismic-reflection profiles on sheet 8 (figs. 1, 2, 3, 4, 6, 7, 9, 10). This post-LGM 

stratigraphic unit is typically characterized either by “acoustic transparency” or by parallel, lowamplitude, low- to high-frequency, continuous to moderately continuous, diffuse reflections 

(terminology from Mitchum and others, 1977). The acoustic transparency (that is, lack of internal 

reflections) can be caused by extensive wave winnowing, resulting in a uniform sediment grain size, 

hence, the lack of acoustic-impedance contrasts needed to produce seismic reflections. The contact 

between these sediments and the underlying strata is a transgressive erosional surface, which commonly 

is marked by angularity, channeling, or a distinct upward change to lower amplitude, more diffuse 

reflections. It is emphasized that the base of this unit is an interpretation somewhat hindered by both 

acoustic transparency and by “acoustic masking,” which is associated with the presence of interstitial 

gas within the sediment (see, for example, Fader, 1997). 

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 Half Moon Bay map area (Maps A, B) and, to 

establish regional context, for a larger area (about 91 km of coast) that extends from the Bolinas area to 

Pescadero Point (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, E) was 

determined by applying a sound velocity of 1,600 m/sec to the TWT, resulting in thicknesses as great as 

about 57 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 San Andreas, San Gregorio, and Golden Gate 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 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) was generated by 

adding the thickness data to water depths determined by multibeam bathymetry (see sheet 1).

The thickness of the post-LGM unit in the Offshore of Half Moon Bay map area ranges from 0 to 

13 m (Map B on sheet 9), and the depth to the base of this unit ranges from less than 10 to 62 m (Map A 
25

on sheet 9). The most rapid changes in thickness are in the northern part of the map area and are 

associated with the west strand of the San Gregorio Fault. Mean sediment thickness for the map area is 

2.5 m, and the total sediment volume is 309×106

 m3 (table 7–1). The relatively thin sediment cover in 

most of the map area suggests a lack of sediment “accommodation space” (Catuneanu, 2006), which is 

consistent with regional uplift. The uplift raises and exposes much of the shallow shelf to the high wave 

energy that is characteristic of this region (Barnard and others, 2007), so that sediments are efficiently 

reworked and transported off the inner shelf and midshelf areas to deeper water.

Five different “domains” of sediment thickness are recognized on the regional sedimentthickness map (Map D on sheet 9): (1) the Bolinas shelf, located west of the east strand of the San 

Gregorio Fault Zone, in the northwestern part of the regional map (Map D); (2) the San Andreas graben, 

located between the San Gregorio Fault Zone and the Golden Gate Fault, east-southeast of the Bolinas 

shelf and both southwest and southeast of the Marin shelf; (3) the Marin shelf, located both northeast 

and northwest of the San Andreas graben and north of the San Francisco ebb-tidal delta paleovalley; (4) 

the northeast-trending San Francisco ebb-tidal delta paleovalley, located outside the Golden Gate at the 

mouth of San Francisco Bay, between the Marin shelf and San Andreas graben on the north and the 

Pacifica-Pescadero shelf on the south; and (5) the Pacifica-Pescadero shelf, which is located south of the 

San Francisco ebb-tidal delta paleovalley and which extends south all the way to Pescadero Point 

(including all of the Offshore of Half Moon Bay map area). 

The five sediment-thickness domains have distinct geologic controls. The Bolinas and PacificaPescadero shelves are uplifting and are relatively sediment poor (mean sediment thicknesses of 0.8 and 

3.6 m, respectively; table 7–1). Thicker sediment accumulations (as much as 20 m) on the western 

margins of the Pacifica-Pescadero shelf (within California’s State Waters) are associated with west-sidedown slip on the west strand of the San Gregorio Fault Zone and with deposition on the outboard, westdipping Pigeon Point block (McCulloch, 1987) (fig. 2 on sheet 9) farther south offshore of Pescadero 

Point. The San Andreas graben is a rapidly subsiding, fault-controlled sedimentary basin that has 

sediment thicknesses of as much as 57 m; the Marin shelf forms the uplifted northeastern and 

northwestern margins of this basin. The San Francisco ebb-tidal delta is filling a paleovalley that formed 

during the last sea-level lowstand, with sediment thicknesses of as much as 32 m along the trough axis. 

Although the southern part of the San Andreas graben may extend into the paleovalley, the north flank 

of the paleovalley is used here as the boundary when calculating sediment volumes for the five 

sediment-thickness domains (table 7–1). Subsidence in the San Francisco ebb-tidal delta paleovalley and 

the San Andreas graben can be partly attributed to the northward change in strike of both the San 

Andreas and San Gregorio Fault Zones offshore of San Francisco, which has resulted in the local change 

from contractional deformation to extensional deformation (Zoback and others, 1999). 

The Bolinas shelf and the San Andreas graben represent the extremes of sediment distribution in 

the Bolinas to Pescadero region (Maps C, D). The San Andreas graben occupies just 5.1 percent of the 

region but contains about 27.6 percent of its sediment. In contrast, the Bolinas shelf occupies 13.6 

percent of the region but contains just 1.8 percent of its sediment. The Pacifica-Pescadero shelf is 

relatively sediment poor, making up 66.3 percent of the region but containing 39.0 percent of its 

sediment.
26

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

Pescadero region (domains 1–5), as well as in Offshore of Half Moon Bay map area.

Regional sediment-thickness domains in Bolinas to Pescadero region

Area (km2) Mean sediment 

thickness (m)

Sediment volume 

(106 m3) 

Entire Bolinas to Pescadero region 529 6.2 3,286

(1) Bolinas shelf, west of east strand of San Gregorio Fault 

Zone 72 0.8 59

(2) San Andreas graben, between San Gregorio Fault Zone and 

Golden Gate Fault 27 33.5 906

(3) Marin shelf, northeast and northwest of San Andreas 

graben, north of San Francisco ebb-tidal delta paleovalley 44 8.1 355

(4) San Francisco ebb-tidal delta paleovalley 35 19.5 685

(5) Pacifica-Pescadero shelf 351 3.6 1,281

Sediment thickness in Offshore of Half Moon Bay map area

Offshore of Half Moon Bay map area 123 2.5 309
27

Chapter 8. Geologic and Geomorphic Map of the Offshore of Half Moon 

Bay Map Area (Sheet 10) 

By H. Gary Greene, Michael W. Manson, Charles A. Endris, and Samuel Y. Johnson

Geologic and Geomorphic Summary

Marine geology and geomorphology were mapped in the Offshore of Half Moon Bay 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). 

Onshore geology was compiled from Brabb and others (1998) and Witter and others (2006). Unit 

ages, which are derived from these sources, reflect local stratigraphic relations.

The continental shelf within California’s State Waters in the Offshore of Half Moon Bay map 

area is shallow (less than about 55 m) and flat with a very gentle (less than 0.5°) offshore dip. Shelf 

morphology and evolution are the result of the interplay between local tectonics and sedimentation as 

sea level rose about 125 to 130 m during the last about 21,000 years (see, for example, Lambeck and 

Chappell, 2001; Gornitz, 2009), leading to the progressive eastward migration (a few tens of kilometers) 

of the shoreline and wave-cut platform and the associated transgressive erosion and deposition (see, for 

example, Catuneanu, 2006). The Offshore of Half Moon Bay map area is now an open-ocean shelf that 

is subjected to full, and sometimes severe, wave energy and strong currents. 

Given the relatively shallow depths and high energy, modern shelf deposits are mostly sand (unit 

Qms). Coarser grained sands and gravels (units Qmss and Qmsc) are recognized primarily on the basis 

of bathymetry and high backscatter (sheets 1, 2, 3). Unit Qmsc is mapped only as a nearshore bar (about 

10 m water depth) just south of the Pillar Point Harbor jetty. Unit Qmss, which typically is mapped as 

erosional lags in scour depressions (see, for example, Cacchione and others, 1984), is more extensive 

and distributed, the largest concentrations found at water depths of 30 to 55 m offshore of Pillar Point, as 

well as in the nearshore (at depths of 5 to 15 m) south of Pillar Point Harbor and north-northwest of 

Pillar Point. 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 (and, thus, is 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. Although the general areas in which both unit Qmss scour depressions 

and unit Qmsc nearshore bars are found are not likely to change substantially, the boundaries of the 

unit(s) likely are ephemeral, changing seasonally and during significant storm events. 

Offshore bedrock outcrops are mapped as the upper Miocene and Pliocene Purisima Formation 

(unit Tp), the Cretaceous granitic rocks of Montara Mountain (unit Kgr), and undifferentiated 

sedimentary rocks of the undivided bedrock unit of Cretaceous and (or) Tertiary age (TKu). These units 

are delineated by extending outcrops and trends from mapped onshore geology and also by their 

distinctive surface textures as revealed by high-resolution bathymetry (see sheets 1, 2). Outcrops of the 

Purisima Formation form distinctive, straight to curved “ribs,” caused by differential erosion of more 

and less resistant lithologies (for example, sandstone and mudstone). In contrast, granitic rocks have a 

densely cross-fractured surface texture. The Offshore of Half Moon Bay map area contains artificial fill 

(unit af) only inside Pillar Point Harbor. 
28

Areas where shelf sediments form thin (2.5 m or less) veneers over low-relief rocks of the 

undivided Cretaceous and (or) Tertiary bedrock unit or the Purisima Formation (upper Miocene and 

Pliocene) are mapped as units Qms/TKu and Qms/Tp, respectively. These composite units are 

recognized on the basis of the combination of flat relief, continuity with moderate- to high-relief 

bedrock outcrops, high-resolution seismic-reflection data (see sheet 8), and (in some cases) moderate to 

high backscatter. Overlying sediment is interpreted as an ephemeral and dynamic sediment layer that 

may or may not be continuously present at a specific location, depending on storms, seasonal and (or) 

annual patterns of sediment movement, or longer term climate cycles. Storlazzi and others (2011) 

described the seasonal burial and exhumation of submerged bedrock in a similar high-energy setting in 

northern Monterey Bay, about 55 km south of the map area. The relative proportions of all offshore map 

units are shown in table 8–1. 

The Offshore of Half Moon Bay map area lies about 12 km southwest of the San Andreas Fault, 

the dominant structure in the distributed, right-lateral, transform boundary between the North American 

and Pacific plates. The map area straddles the right-lateral San Gregorio Fault system, a prominent 

structure west of the San Andreas Fault in the broader San Andreas Fault system. The San Gregorio 

Fault system extends for about 400 km from Point Conception on the south to Bolinas and Point Reyes 

on the north (Dickinson and others, 2005), predominantly in the offshore but also onshore at coastal 

promontories such as Pillar Point in the map area and also at Pescadero Point, about 15 km south of the 

map area (see Map E on sheet 9). 

In the Offshore of Half Moon Bay map area, the San Gregorio Fault system forms a distributed 

shear zone about 2 to 4.5 km wide that includes two main diverging fault strands (fig. 1 on sheet 10). 

The east strand (also known as the Seal Cove Fault or Coastways Fault), which roughly parallels the 

shoreline, extends onshore for about 3 km at Pillar Point, locally forming the boundary between 

outcrops of Cretaceous granitic rocks to the east and the Purisima Formation to the west. The west 

strand (also known as the Frijoles Fault), which lies entirely offshore, forms a boundary between the 

Purisima Formation on the east and undivided Cretaceous and (or) Tertiary rocks of the Pigeon Point 

block (McCulloch, 1987) (fig. 1 on sheet 10) on the west. The Pigeon Point block is a northwesttrending bedrock ridge that extends offshore of Pescadero for about 30 km and forms the northwest 

boundary of the Outer Santa Cruz Basin. 

Table 8–1. Areas and relative proportions of offshore geologic map units in Offshore of Half Moon Bay map area.

Map Unit Area (m2) Area (km2) Percent of total area

Marine sedimentary units

Qms 46,167,829 46.17 35.53

Qmsc 688,821 0.69 0.53

Qmss 5,906,449 5.91 4.55

Total, sedimentary units 52,763,099 52.76 40.61

Marine bedrock and (or) shallow bedrock units

Qms/Tp 20,255,887 20.26 15.59

Qms/TKu 1,579,076 1.58 1.22

Tp 54,214,557 54.21 41.72

TKu 292,980 0.29 0.23

Kgr 830,518 0.83 0.64

Total, bedrock units 77,173,018 77.17 59.39

Total, Offshore of Half Moon Bay map area 129,936,117 129.94 100.00
29

Bathymetric data (see sheets 1, 2) and seismic-reflection profiles (see sheet 8) reveal that the 

offshore exposures of the Purisima Formation between the east and west strands of the San Gregorio 

Fault Zone have been spectacularly folded, faulted, and rotated by strike-slip motion and drag along the 

faults. Cumulative lateral slip on the San Gregorio Fault system is thought to range from 4 to 10 mm/yr 

in this area (U.S. Geological Survey and California Geological Survey, 2010). 

The entire map area lies along strike with the young, high topography of the Santa Cruz 

Mountains and Coast Ranges (see sheet 9). This regional uplift has been linked to a northwesttranspressive bend in the San Andreas Fault (see, for example, Zoback and others, 1999). Rates of uplift 

of marine terraces of as much as 0.44 mm/yr near Año Nuevo, 30 km south of the map area, confirms 

that regional uplift is ongoing and that it includes the coastal zone (Weber, 1990). 

DESCRIPTION OF MAP UNITS

OFFSHORE GEOLOGIC AND GEOMORPHIC UNITS

[Note that, where older units (typically, bedrock) are overlain by thin (<1 m thick) Quaternary deposits, 

composite units are mapped. These composite units, which are shown with gray stipple pattern on older 

unit, are designated by composite label indicating both overlying sediment cover and lower (older) unit, 

separated by slash (for example, Qms/Tp indicates that thin sheet of Qms overlies Tp)]

af Artificial fill and anthropogenic material (late Holocene)—Rock, sand, and mud. Placed, 

dredged, or substantially modified by human activity; includes pipelines

Qms Marine nearshore and shelf deposits (late Holocene)—Predominantly sand (some mud); 

ripple marks common; found on seaward-dipping surface that extends from shoreline 

to west edge of map area

Qmss Marine shelf scour depressions (late Holocene)—Inferred to be coarse sand and possibly 

gravel; found as single depressions or in fields of depressions adjacent to bedrock or 

interspersed with elevated shelf sediments (unit Qms). 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 of unit Qms) likely are ephemeral, 

changing during significant storm events 

Qmsc Coarse-grained marine nearshore and shelf deposits (late Holocene)—Predominantly 

coarse sand, gravel, cobbles, and boulders; found on gently seaward-dipping (less 

than 1o) surface in water depths typically less than about 20 m; recognized primarily 

on basis of variable and mottled backscatter

Tp Purisima Formation (Pliocene and late Miocene)—Predominantly gray and greenish-gray 

to buff, fine-grained marine sandstone, siltstone, and mudstone; also includes some 

porcelaneous shale and mudstone, chert, silty mudstone, and volcanic ash. Stippled 

areas (composite unit Qms/Tp) indicate where thin sheets of Qms overlie unit 

TKu Bedrock, undivided (Tertiary and (or) Cretaceous)—Stippled areas (composite unit 

Qms/TKu) indicate where thin sheets of Qms overlie unit 

Kgr Granitic rocks of Montara Mountain (Cretaceous)—Medium-crystalline to coarsely 

crystalline, foliated granitic rock; largely quartz diorite with some granite 
30

ONSHORE GEOLOGIC AND GEOMORPHIC UNITS

[Units are compiled from Brabb and others (1998) and Witter and others (2006); unit ages, which are 

from these sources, reflect local stratigraphic relations. Locations of some faults from California 

Geological Survey (1976, 1982, 2002b)]

af Artificial fill (late Holocene)—Rock, sand, and mud; material deposited by humans 

afem Artificial fill over estuarine mud (late Holocene)—Material deposited by humans over 

estuarine sediments 

adf Artificial-dam fill (late Holocene)—Earth- or rock-fill dams, embankments, and levees; 

constructed to impound land-locked water bodies 

alf Artificial-levee fill (late Holocene)—Artificial levees bordering rivers, streams, salt ponds, 

and sloughs; constructed to contain floodwater or tidal waters 

Qf Alluvial fan deposits (late Holocene)—Alluvial fan deposits; judged to be late Holocene 

(<1,000 years) in age, on basis of records of historical inundation or presence of 

youthful braid bars and distributary channels 

Qc 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 

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

Qyf Alluvial fan deposits (Holocene)—Sediment deposited by streams emanating from 

mountain canyons onto alluvial valley floors or alluvial plains; includes debris-flow, 

hyperconcentrated-mudflow, and braided-stream deposits

Qt2 Stream-terrace deposits (Holocene)—Relatively smooth, undissected terraces less than 8 to 

10 m above active channel; younger than unit Qt1

Qt1 Stream-terrace deposits (Holocene)—Relatively smooth, undissected terraces less than 8 to 

10 m above active channel; older than unit Qt2

Qa Alluvial deposits, undivided (Holocene)—Alluvium; deposited in fan, terrace, or basin 

environments 

Qcl Colluvium (Holocene)—Loose to firm, unsorted sand, silt, clay, gravel, rock debris, and 

organic material, in varying proportions 

Qof2 Older 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, as well as where deposits might be of either Holocene or late Pleistocene age

Qls Landslide deposits (Holocene and Pleistocene)—Disintegrated bedrock; physically 

weathered; ranges from deep-seated landslides to active colluvium 

Qof1 Older alluvial fan deposits (late Pleistocene)—Alluvial fans; late Pleistocene age is 

indicated by degree of dissection or soil development greater than what is present on 

Holocene fans

Qot Older stream-terrace deposits (late Pleistocene)—Relatively flat, slightly dissected stream 

terraces; late Pleistocene age is indicated by degree of soil development and height of 

terrace above flood level

Qoa Older alluvial deposits, undivided (late Pleistocene)—Mapped on gently sloping to level 

alluvial fan or terrace surfaces or where separate units could not be delineated at map

scale; late Pleistocene age is indicated by depth of stream incision, degree of soil 

development, and lack of historical flooding 
31

Qmt Marine-terrace deposits, undivided (Pleistocene)—Sand and gravel, deposited on uplifted 

marine-abrasion platforms along coast. Local relative ages designated by numbers 

from youngest (Qmt4) to oldest (Qmt1) 

Qmt4 Marine-terrace deposits (Pleistocene)—Sand and gravel, deposited on uplifted marineabrasion platforms along coast

Qmt3 Marine-terrace deposits (Pleistocene)—Sand and gravel, deposited on uplifted marineabrasion platforms along coast 

Qmt2 Marine-terrace deposits (Pleistocene)—Sand and gravel, deposited on uplifted marineabrasion platforms along coast 

Qmt1 Marine-terrace deposits (Pleistocene)—Sand and gravel, deposited on uplifted marineabrasion platforms along coast 

Tp Purisima Formation, undivided (Pliocene and late Miocene)—Medium-grained to very 

fine-grained, poorly indurated to friable sandstone, siltstone, and claystone, with 

conglomerate lenses and a few beds of white volcanic ash

Tptu Tunitas Sandstone Member (Pliocene)—Fine-grained sandstone, siltstone, and 

mudstone; some porcelaneous shale and mudstone, chert, silty mudstone, and 

volcanic ash

Tpl Lobitos Mudstone Member (Pliocene)—Massive silty mudstone 

Tpsg San Gregorio Sandstone Member (Pliocene)—Fine- to coarse-grained sandstone that 

has calcareous concretions 

Tpp Pomponio Mudstone Member (Pliocene)—Porcelaneous shale and mudstone; in 

places, rhythmically bedded with alternating layers of nonsiliceous mudstone 

Tpt Tahana Member (Pliocene and late Miocene)—Medium-grained to very fine-grained 

lithic sandstone and siltstone, interbedded with some silty mudstone, tuffaceous 

sandstone, and pebble conglomerate

Tm Monterey Formation (Miocene)—Porcelaneous shale with chert, porcelaneous mudstone, 

impure diatomite, and calcareous claystone, as well as small amounts of siltstone and 

sandstone near base 

Tlo Lompico Sandstone (Miocene)—Fine- to coarse-grained, well-cemented arkosic sandstone 

Tss Unnamed sandstone, shale, and conglomerate (Paleocene)—Rhythmically alternating 

beds of sandstone and shale, with discontinuous boulder and cobble conglomerate 

lenses near middle of section and some pebble conglomerate beds near base of 

section on Montara Mountain 

Kgr Granitic rocks of Montara Mountain (Cretaceous)—Very light gray to light-brown, 

medium-crystalline to coarsely crystalline, foliated granitic rock; largely quartz 

diorite with some granite; highly fractured and deeply weathered

KJf Franciscan Complex, undivided (Cretaceous and Jurassic)—Mostly graywacke and 

shale. Locally divided into following subunits: 

fs Sandstone—Greenish-gray to buff, fine- to coarse-grained sandstone (graywacke), with 

interbedded siltstone and shale 

fg Greenstone—Dark-green to red, altered basaltic rocks, including flows, pillow lavas, 

breccias, tuff breccias, tuffs, and minor related intrusive rocks 

fl Limestone—Light-gray, finely to coarsely crystalline limestone in lenticular bodies; 

generally surrounded by Franciscan greenstone 

m Marble and hornfels blocks (Paleozoic?)—Finely crystalline marble, graphitic marble, 

and quartz-mica hornfels
32

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 Fulmar, National Oceanic and Atmospheric 

Administration’s Monterey Bay National Marine Sanctuary—for their skill and professionalism in 

collecting the data presented in this report. We thank Brian Edwards and Michael Fisher (both 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. 
33

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