| Alameda Creek, San Francisco Bay, California | Alameda Naval Air Station fuel pier, San Francisco Bay, California | Alameda, San Francisco Bay, California | Alcatraz Island, San Francisco Bay, California | Angel Island (west side), San Francisco Bay, California | Angel Island, East Garrison, San Francisco Bay, California | Ano Nuevo Island, California | Antioch, San Joaquin River, California | Arcata Wharf, Humboldt Bay, California | Arena Cove, California | Avalon, Santa Catalina Island, California | A |
| Balboa Pier, Newport Beach, California | Ballast Point, California | Bay Slough, east end, San Francisco Bay, California | Bay Slough, west end, San Francisco Bay, California | Bechers Bay, Santa Rosa Island, California | Benicia, California | Berkeley, San Francisco Bay, California | Bishop Cut, Disappointment Slough, San Joaquin River, California | Blackslough Landing, San Joaquin River, California | Blakes Landing, Tomales Bay, California | Bodega Harbor entrance, California | Bolinas, Bolinas Lagoon, California | Borden Highway Bridge, Middle River, San Joaquin River, California | Borden Highway Bridge, Old River, San Joaquin River, California | Borden Highway Bridge, San Joaquin River, California | Brazos Drawbridge, Napa River, California | Bucksport, Humboldt Bay, California | B |
| Cabrillo Beach, California | Calaveras Point, west of, San Francisco Bay, California | Carmel Cove, Carmel Bay, California | Catalina Harbor, Santa Catalina Island, California | Chevron Oil Company Pier, Richmond, San Francisco Bay, California | Clarksburg, Sacramento River, California | Cockrobin Island Bridge, Eel River, San Francisco, California | Collinsville, Sacramento River, California | Corkscrew Slough, San Francisco Bay, California | Corte Madera Creek, San Francisco Bay, California | Coyote Creek, Alviso Slough, San Francisco Bay, California | Coyote Creek, Tributary No. 1, San Francisco Bay, California | Coyote Hills Slough entrance, San Francisco Bay, California | Coyote Point Marina, San Francisco Bay, California | Crescent City, California | Crockett, Carquinez Strait, California | Crown Point, Mission Bay, California | Cuyler Harbor, San Miguel Island, California | C |
| Davis Slough, San Joaquin River, California | Drakes Bay, Point Reyes, California | Dumbarton Highway Bridge, San Francisco Bay, California | D |
| Edgerley Island, Napa River, California | El Segundo, Santa Monica Bay, California | Elk River Railroad Bridge, Humboldt Bay, California | Elkhorn Slough at Elkhorn, Monterey Bay, California | Elkhorn Slough railroad bridge, Monterey Bay, California | Elkhorn Slough, Highway 1 Bridge, Monterey Bay, California | Elkhorn Yacht Club, Monterey Bay, California | Eureka Slough Bridge, Humboldt Bay, California | Eureka, Humboldt Bay, California | E |
| False River, San Joaquin River, California | Fields Landing, Humboldt Bay, California | Fort Bragg Landing, California | Fort Ross, California | F |
| Gallinas, Gallinas Creek, San Pablo Bay, California | Gaviota State Park, California | Gaviota, California | General Fish Company Pier, Moss Landing, Monterey Bay, California | Georgiana Slough entrance, Mokelumne River, California | Gold Street Bridge, Alviso Slough, San Francisco Bay, California | Granite Rock, Redwood Creek, San Francisco Bay, California | Grant Line Canal (drawbridge), San Joaquin River, California | Green Cove, California | G |
| Hercules, Refugio Landing, San Pablo Bay, California | Hog Island, San Antonio Creek, San Pablo Bay, California | Holt, Whiskey Slough, San Joaquin River, California | Hookton Slough, Humboldt Bay, California | Hunters Point, San Francisco Bay, California | H |
| Imperial Beach, California | Inverness, Tomales Bay, California | Irish Landing, Sand Mound Slough, San Joaquin River, California | I |
| Joice Island, Suisun Slough, Suisun Bay, California | J |
| King Harbor, Santa Monica Bay, California | Kirby Park, Elkhorn Slough, Monterey Bay, Port San Luis, California | Korths Harbor, San Joaquin River, California | K |
| La Jolla (Scripps Institution Wharf), California | Lakeville, Petaluma River, California | Lakeville, Petaluma River, San Pablo Bay, California | Long Beach, Inner Harbor, California | Long Beach, Terminal Island, California | Los Angeles (outer harbor), California | Los Angeles Harbor, Mormon Island, California | Los Patos (highway bridge), California | L |
| Mad River Slough, Arcata Bay, Humboldt Bay, California | Mallard Island Ferry Wharf, Suisun Bay, California | Mansfield Cone, California | Mare Island Naval Shipyard, Carquinez Strait, California | Marshall, Tomales Bay, California | Martinez-Amorco Pier, California | Meins Landing, Montezuma Slough, Suisun Bay, California | Mendocino, Mendocino Bay, California | Mission Bay, California | Monterey, Monterey Harbor, California | Montezuma Slough Bridge, Suisun Bay, California | Montezuma Slough, Suisun Bay, California | Mowry Slough, San Francisco Bay, California | Mugu Lagoon (ocean pier), California | M |
| Napa, Napa River, California | National City, San Diego Bay, California | New Hope Bridge, Mokelumne River, California | Newark Slough, San Francisco Bay, California | Newport Beach, Newport Bay entrance, Corona del Mar, California | North Point, Pier 41, San Francisco, San Francisco Bay, California | North Spit, Humboldt Bay, California | Noyo Harbor, Fort Bragg, California | Noyo River, California | Nurse Slough, Bradmoor Island, Suisun Bay, California | N |
| Oakland Airport, San Francisco Bay, California | Oakland Berth 67, San Francisco Bay, California | Oakland Harbor, Grove Street, San Francisco Bay, California | Oakland Harbor, Park Street Bridge, San Francisco Bay, California | Oakland Inner Harbor, San Francisco Bay, California | Oakland Middle Harbor, San Francisco Bay, California | Oakland Pier, San Francisco Bay, California | Oakland, Matson Wharf, San Francisco Bay, California | Ocean Beach, outer coast, California | Ocean Pier, Moss Landing, Monterey Bay, California | Oil Platform Harvest (Topex Project), California | Orwood, Old River, San Joaquin River, California | Oyster Point Marina, San Francisco Bay, California | O |
| Pacific Mariculture Dock, Elkhorn Slough, Monterey Bay, California (sub) | Pacific Mariculture Dock, Monterey Bay, California | Palo Alto Yacht Harbor, San Francisco Bay, California | Petaluma River entrance, San Pablo Bay, California | Pierce Harbor, Goodyear Slough, Suisun Bay, California | Pillar Point Harbor, Half Moon Bay, California | Pinole Point, San Pablo Bay, California | Pittsburg, New York Slough, Suisun Bay, California | Point Arena, California | Point Arguello, California | Point Bonita, Bonita Cove, San Francisco Bay, California | Point Buckler, Suisun Bay, California | Point Chauncey, San Francisco Bay, California | Point Isabel, San Francisco Bay, California | Point Loma, California | Point Orient, San Francisco Bay, California | Point San Bruno, San Francisco Bay, California | Point San Pedro, San Pablo Bay, California | Point San Quentin, San Francisco Bay, California | Port Chicago, Suisun Bay, California | Port Hueneme, California | Port San Luis, California | Port San Luis, Pacific Ocean, California | Potrero Point, San Francisco Bay, California | Princeton, Half Moon Bay, California | Prisoners Harbor, Santa Cruz Island, California | Prisoners Point, San Joaquin River, California | Pyramid Point, Smith River, California | P |
| Quivira Basin, Mission Bay, California | Q |
| Redwood City, Wharf 5, San Francisco Bay, California | Redwood Creek Marker 8, San Francisco Bay, California | Redwood Creek entrance (inside), San Francisco Bay, California | Requa Dock, California | Reynolds, Tomales Bay, California | Richmond Inner Harbor, San Francisco Bay, California | Rincon Island, Mussel Shoals, Santa Barbara Channel, California | Rincon Point, Pier 22½, San Francisco Bay, California | Rio Vista, Sacramento River, California | Roberts Landing, 1.3 mi west of, San Francisco Bay, California | R |
| Sacramento, Sacramento River, California | Samoa, Humboldt Bay, California | San Clemente, California | San Diego, Quarantine Station, California | San Diego, San Diego Bay, California | San Francisco Bar, California | San Francisco, San Francisco Bay, California | San Leandro Channel, San Leandro Bay, San Francisco Bay, California | San Leandro Marina, San Francisco Bay, California | San Mateo Bridge (east end), San Francisco Bay, California | San Mateo Bridge (west end), San Francisco Bay, California | San Nicolas Island, California | San Simeon, California | Santa Ana River entrance (inside), California | Santa Barbara Island, California | Santa Barbara, California | Santa Barbara, Pacific Ocean, California | Santa Cruz, Monterey Bay, California | Santa Cruz, Monterey Bay, California (sub) | Santa Monica, Municipal Pier, California | Santa Monica, Municipal Pier, San Pedro Channel, California | Sausalito, Corps of Engineers Dock, San Francisco Bay, California | Sausalito, San Francisco Bay, California | Seaplane Harbor, San Francisco Bay, California | Selby, California | Shelter Cove, California | Smith Slough, San Francisco Bay, California | Snodgrass Slough, Sacramento River, California | Sonoma Creek, San Pablo Bay, California | South Bay Wreck, San Francisco Bay, California | South San Diego Bay, California | South San Francisco, San Francisco Bay, California | Southeast Farallon Island, California | Steamboat Slough, Snug Harbor Marina, Sacramento River, California | Stockton, San Joaquin River, California | Suisun City, Suisun Slough, Suisun Bay, California | Suisun Slough entrance, Suisun Bay, California | S |
| Terminous, South Fork, Mokelumne River, California | Threemile Slough entrance, San Joaquin River, California | Threemile Slough, Sacramento River, California | Tidal Creek, Elkhorn Slough, Monterey Bay, Port San Luis, California | Tomales Bay entrance, California | Trinidad Harbor, California | T |
| Upper Guadalupe Slough, San Francisco Bay, California | Upper drawbridge, Petaluma River, San Pablo Bay, California | U |
| Vallejo, Mare Island Strait, California | Ventura, California | V |
| Wards Island, Little Connection Slough, San Joaquin River, California | West Point Slough, San Francisco Bay, California | Westport, California | Wilson Cove, San Clemente Island, California | Wingo, Sonoma Creek, San Pablo Bay, California | W |
| Yerba Buena Island, San Francisco Bay, California | Y |
