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- Bacon Island
- Banta
- Banta Carbona Canal
- Bardi
- Bear Creek
- Beaver Slough
- Beaver Slough
- Bethany
- Bishop Cut
- Black Slough
- Boscha Lake (historical)
- Bouldin Island
- Browns Island
- Buckley Cove
- Burnham
- Burns Cutoff
- Burns Reach
- Calaveras River
- Campbell Lateral
- Carnazzani Island (historical)
- Chappel Lateral
- Cherokee
- Clark Lateral
- Collierville
- Columbia Cut
- Connection Slough
- Corral Hollow Creek
- Country Club
- Coyote Creek
- Criminal Slough
- Fabian and Bell Canal
- Fairbanks Lateral
- Farmington
- Farmington Flood Control Basin
- Farmington Lake
- Fay Island
- Fern Island
- Fivemile Creek
- Fivemile Slough
- Forest Lake
- Fourteenmile Slough
- French Camp
- French Camp Slough
- Haight
- Hayes Point
- Hayes Reach
- Hayes Slough
- Haypress Reach
- Headreach Cutoff
- Headreach Island
- Henderson Village
- Hetch Hetchy Aqueduct
- Hirshfield Lateral
- Hog Island
- Hog Island Cut
- Hog Slough
- Holman Slough (historical)
- Holt
- Homestead Canal
- Honker Cut
- Huffman Lateral
- Lake Lincoln
- Lake Venezia
- Lateral Five East
- Lateral Five West
- Lateral Four West
- Lateral Six East
- Lateral Three West
- Latham Slough
- Lathrop
- Lincoln Village West Marina
- Linden
- Little Connection Slough
- Little Mandeville Island
- Little Potato Slough
- Little Venice Island
- Littlejohns Creek
- Lockeford
- Lodi
- Lone Tree Creek
- Lone Tree Creek
- Lower Main Canal
- Lyoth
- Main District Canal
- Mandeville Cut
- Mandeville Island
- Mandeville Point
- Mandeville Reach
- Manteca
- Manteca Junction
- McDonald Island
- McLeod Lake
- Meadow Lake
- Medford Island
- Middle Fork Lone Tree Creek
- Middle Paddy Creek
- Middle River
- Midway
- Mildred Island
- Mokelumne Aqueduct
- Mokelumne Beach
- Mokelumne River
- Morada
- Mormon Slough
- Mosher Creek
- Mosher Slough
- Mossdale
- Mossdale Marina
- Mountain House
- Mountain House Creek
- Murphy Creek
- Nibs Slough
- North Canal
- North Fork Duck Creek
- North Lake
- North Mokelumne River
- North Victoria Canal
- Northwest Main Canal
- Paddy Creek
- Paradise Cut
- Paradise Point
- Patterson Run
- Pegleg Creek
- Peters
- Pixley Slough
- Port of Stockton
- Potato Point
- Potato Slough
- Prisoners Point
- Pumping Station Number One
- Salmon Slough
- San Joaquin River Club
- Shenkel Island
- Shima Bend
- Singapore Cut
- Smith Canal
- Smith Lake
- South Main Canal
- South Mokelumne River
- South Paddy Creek
- Spud Island
- Stanislaus River
- Staten Island
- Stockton
- Stockton Deep Water Channel
- Stockton Diverting Canal
- Sturgeon Bend
- Sugar Cut
- Summer Home
- Sweet Lateral
- Sycamore Slough
- Taft Mosswood
- Telephone Cut
- Tenmile Slough
- Terminous
- Thornton
- Three River Reach
- Tinsley Island
- Tom Paine Slough
- Tracy
- Tracy Lake
- Trapper Slough
- Trull
- Tule Island
- Turner
- Turner Cut
- Turner Lake (historical)
- Turner Slough (historical)
- Twentyone Mile Cut
- Venice Cut
- Venice Island
- Venice Reach
- Vernalis
- Victor
- Victoria Canal
- Victoria Island
- Villinger
- Vulcan Island