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- Acalanes Ridge (populated place)
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- Alamo Creek (stream)
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- Antioch City Marina (marina)
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- East Branch Green Valley Creek (stream)
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- Franklin Creek (stream)
- Frog Pond (lake)
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- Green Valley Creek (stream)
- Grizzly Creek (stream)
- Hammer Island (island)
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- Kellogg Creek (stream)
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- Lafayette Creek (stream)
- Lafayette Reservoir (reservoir(s))
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- Las Trampas Creek (stream)
- Lauritzen Canal (canal)
- Lauritzen Yacht Harbor (harbor(s))
- Lauterwasser Creek (stream)
- Leland Reservoir (reservoir(s))
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- Little Pine Creek (stream)
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- Martinez Reservoir (reservoir(s))
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- Middle Slough (channel)
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- Moraga Reservoir (reservoir(s))
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- New York Slough (channel)
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- Pacheco Creek (stream)
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- Pinole Creek (stream)
- Pinole Point (cape)
- Pinole Shoal (bar)
- Pinole Shoal Channel (channel)
- Piper Slough (inlet)
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- Pittsburg Marina (marina)
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- Point Edith Crossing Range (channel)
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- Refugio Creek (stream)
- Reliez Highlands-Hidden Pond (city)
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- Richmond Harbor Entrance Channel (channel)
- Richmond Inner Harbor (bay)
- Richmond Marina Bay (harbor(s))
- Richmond Yacht Harbor (harbor(s))
- Rock City (city)
- Rock Slough (stream)
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- Rodeo Creek (stream)
- Rodeo Marina (marina)
- Rollingwood (populated place)
- Roosevelt Cut (canal)
- Russellmann Creek (stream)
- Sacramento River (stream)
- Saint Marys Bay (bay)
- San Catanio Creek (stream)
- San Joaquin Harbor (harbor(s))
- San Joaquin River (stream)
- San Pablo (city)
- San Pablo Creek (stream)
- San Pablo Reservoir (reservoir(s))
- San Pablo Strait (channel)
- San Ramon (city)
- San Ramon Creek (stream)
- Sand Bay (bay)
- Sand Creek (stream)
- Sand Mound Slough (inlet)
- Sandpiper Spit (bar)
- Santa Clara Shoal (bar)
- Santa Fe Channel (channel)
- Saranap (city)
- Seal Creek (stream)
- Seal Island Channel (channel)
- Seal Islands (island)
- Selby (city)
- Selby Reservoir (reservoir(s))
- Serpents Slough (inlet)
- Sheep Slough (inlet)
- Short Slough (inlet)
- Sindicich Lagoons (lake)
- Sobrante Reservoir (reservoir(s))
- Southampton Shoal North Buoy (historical) (beacon)
- Stake Point (cape)
- Stewartville (city)
- Suisun Point (cape)
- Summit Reservoir (reservoir(s))
- Sycamore Creek (stream)
- Sycamore Creek (stream)
- Tara Hills (city)
- Tassajara (city)
- Taylor Slough (inlet)
- The Brothers (island)
- Tice Creek (stream)
- Tice Valley Area (city)
- Tin House Cove (bay)
- Waldon (city)
- Walnut Creek (stream)
- Walnut Creek (city)
- Webb Point (cape)
- Webb Reach (channel)
- Werner Dredger Cut (canal)
- West Branch Alamo Creek (stream)
- West Canal (canal)
- West Reach (channel)
- Whiting Rock (bar)
- Widdows Island (island)
- Wildcat Creek (stream)
- Willow Lake (reservoir(s))
- Wilson Point (cape)
- Winter Island (island)