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- Irvington Pumping Station (water pumping station)
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- Middlefield Reservoir (reservoir(s))
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- Reservoir Number One (reservoir(s))
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- Salt Pond A19 (reservoir(s))
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- San Lorenzo Creek (stream)
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- Sheridan Creek (stream)
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- Small Boat Lagoon (bay)
- South Bay Aqueduct (canal)
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- Stonybrook Creek (stream)
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- Sunol Aqueduct (canal)
- Swimming Lagoon (reservoir(s))
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- Temescal Creek (stream)
- Terrace Point (cape)
- Thirtyninth Avenue Reservoir (reservoir(s))
- Tidal Canal (canal)
- Toroges Creek (stream)
- Tracy Pumping Station (water pumping station)
- Trout Creek (stream)
- Tule Pond (reservoir(s))
- Tyson Lake (reservoir(s))