Sub-tidal benthic habitats of central San Francisco Bay and offshore Golden Gate area: A review

Deep-water potential estuarine and marine benthic habitat types were defined from a variety of new and interpreted data sets in central San Francisco Bay and offshore Golden Gate area including multibeam echosounder (MBES), side-scan sonar and bottom grab samples. Potential estuarine benthic habitats identified for the first time range from hard bedrock outcrops on island and mainland flanks and some Bay floor
regions, to soft, very dynamic bedforms consisting of sediment waves and ripples. Soft sediment ranges from mud and sand to bimodal (two or more grain sizes) sediment of gravel, pebbles, and cobbles. In addition, considerable anthropogenic features (i.e., pipelines, bridge abutments, dredged channels, dump sites) were distinguished.

Of the 52 potential benthic habitat types mapped (compressed to 14 types for this paper), 24 were of un-consolidated sediment with five of these comprised of dynamic bedforms or sediment waves and dunes, five of mixed (soft over hard) substrate type, six of hard substrate or rock outcrop, 13 of anthropogenically disturbed areas and four hard anthropogenic features. Rock outcrops and rubble are considered the primary habitat type for rockfish (Sebastes spp.), lingcod (Ophiodon elongatus) and in shallow water for
herring (Clupea pallasii) spawning. Dynamic bedforms such as sand waves are considered potential foraging habitat for juvenile lingcod, may be sub-tidal habitat for the Pacific sand lance (Ammodytes
hexapterus) forage fish, and possibly resting habitat for migratory fishes such as sturgeon (Acipenser
medirostris).

The potential marine benthic habitats identified in San Francisco Bay are not unlike those found in other
estuaries around the world and this study should contribute significant information that will be of interest
to scientists, managers and fishers investigating and utilizing bay and estuarine resources. As described in
the many papers of this special issue, the understanding of the interrelationship of geology and ecology is
critical to the identification of essential habitats and the sustainability of a healthy ecosystem.