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- Ackerson Creek (stream)
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- Algerine Creek (stream)
- Algerine Ditch (canal)
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- Andrews Lake (lake)
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- Columbia Ditch (canal)
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- Cow Meadow Lake (lake)
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- Dardanelles Creek (stream)
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- Deer Lake (lake)
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- Don Pedro Reservoir (reservoir(s))
- Donnell Lake (reservoir(s))
- Dorothy Lake (lake)
- Douglas Creek (stream)
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- Dry Meadow Creek (stream)
- Duckwall Creek (stream)
- Dyer Creek (stream)
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- Eagle Creek (stream)
- Eagle Island (historical) (island)
- East Fork Cherry Creek (stream)
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- Edith Lake (lake)
- Eleanor Creek (stream)
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- Harden Lake (lake)
- Hatch Creek (stream)
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- Hells Hollow Creek (stream)
- Herring Creek (stream)
- Herring Creek Reservoir (reservoir(s))
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- Hetch Hetchy Reservoir (reservoir(s))
- High Emigrant Lake (lake)
- Highland Creek (stream)
- Hobart Creek (stream)
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- Horseshoe Bend (stream bend)
- Huckleberry Lake (lake)
- Hull Creek (stream)
- Hunter Bend (stream bend)
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- Hyatt Lake (lake)
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- Ireland Creek (stream)
- Ireland Lake (lake)
- Irwin Bright Lake (lake)
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- Jamestown Ditch (canal)
- Jawbone Creek (stream)
- Jawbone Pass Pond (lake)
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- Kanaka Creek (stream)
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- Kennedy Creek (stream)
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- Kibbie Creek (stream)
- Kibbie Lake (lake)
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- Kole Lake (lake)
- Kuna Creek (stream)
- Kuna Lake (lake)
- La Grange (city)
- La Grange Reservoir (reservoir(s))
- Lake Eleanor (reservoir(s))
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- Lakewood Park Lake (reservoir(s))
- Lambert Lake (lake)
- Lateral B (canal)
- Laurel Lake (lake)
- Leighton Lake (lake)
- Leland Creek (stream)
- Leland Reservoir (reservoir(s))
- Leopold Lake (lake)
- Lertora Lake (lake)
- Lewis Lakes (lake)
- Lily Creek (stream)
- Lily Lake (lake)
- Lion Creek (stream)
- Little Bear Lake (lake)
- Little Beaver Creek (stream)
- Little Jackass Creek (stream)
- Little Otter Lake (lake)
- Little Reynolds Creek (stream)
- Long Barn (city)
- Long Gulch Creek (stream)
- Long Lake (lake)
- Long Valley Creek (stream)
- Looney Creek (stream)
- Lost Creek (stream)
- Lost Lake (lake)
- Lower Cherry Aqueduct (historical) (canal)
- Lukens Lake (lake)
- Lyons Creek (stream)
- Lyons Reservoir (reservoir(s))
- Maclure Creek (stream)
- Maclure Lake (lake)
- Mahan Lake (lake)
- Main Tuolumne Ditch (canal)
- Mann Creek (stream)
- Many Island Lake (lake)
- Martinez (city)
- Mary Lake (lake)
- Matelot Reservoir (reservoir(s))
- Matterhorn Creek (stream)
- Mattie Lake (lake)
- Maxwell Lake (lake)
- McCabe Creek (stream)
- McCabe Lakes (lake)
- McCormick Creek (stream)
- McCormick Creek (stream)
- McGee Lake (lake)
- Mi-Wuk Village (city)
- Middle Branigan Lake (lake)
- Middle Emigrant Lake (lake)
- Middle Emigrant Lake (reservoir(s))
- Middle Fork Stanislaus River (stream)
- Middle Tuolumne River (stream)
- Miguel Creek (stream)
- Mill Creek (stream)
- Mill Creek (stream)
- Miller Lake (lake)
- Miwok Lake (lake)
- Moccasin (city)
- Moccasin Creek (stream)
- Moccasin Reservoir (reservoir(s))
- Mono Vista (city)
- Mormon Creek (stream)
- Morrison Creek (stream)
- Mosquito Lake (lake)
- Mountain Pass Creek (stream)
- Mud Lake (lake)
- Murdock Lake (lake)
- Neall Lake (lake)
- Niagara Creek (stream)
- Niagara Creek (stream)
- North Fork (stream)
- North Fork Griswold Creek (stream)
- North Fork Tuolumne River (stream)
- O'Neil Ditch (canal)
- O'Neil Reservoir (reservoir(s))
- Olive Lake (lake)
- Onion Lake (lake)
- Otter Bar (bar)
- Otter Lake (lake)
- Owl Creek (stream)
- Paddle Creek (stream)
- Parker Pass Creek (stream)
- Parker Pass Lake (lake)
- Peninsula Lake (lake)
- Peoria Creek (stream)
- Peppermint Creek (stream)
- Philadelphia Ditch (canal)
- Phoenix Ditch (canal)
- Phoenix Lake (populated place)
- Phoenix Reservoir (reservoir(s))
- Pine Mountain Lake (reservoir(s))
- Pinecrest Lake (reservoir(s))
- Pingree Lake (lake)
- Pinto Lakes (lake)
- Piute Creek (stream)
- Piute Creek (stream)
- Piute Lake (lake)
- Powell Lake (lake)
- Priest (city)
- Priest Reservoir (reservoir(s))
- Pruitt Lake (lake)
- Rafferty Creek (stream)
- Rancheria Creek (stream)
- Rattlesnake Creek (stream)
- Rawhide (city)
- Red Can Lake (lake)
- Red Mountain Bar Siphon (canal)
- Reed Creek (stream)
- Register Creek (stream)
- Regulation Creek (stream)
- Relief Creek (stream)
- Relief Reservoir (reservoir(s))
- Return Creek (stream)
- Return Lake (lake)
- Rhodes Lake (lake)
- Richards Creek (stream)
- Ridge Lake (lake)
- Rock Creek (stream)
- Rock Creek (stream)
- Rock Island Lake (lake)
- Rodgers Lake (lake)
- Roger Creek (stream)
- Roosevelt Lake (lake)
- Rosasco Lake (lake)
- Rose Creek (stream)
- Rough and Ready Creek (stream)
- Rush Creek (stream)
- Rush Creek (stream)
- Russell Creek (stream)
- Saddle Horse Lake (lake)
- Salt Spring Creek (stream)
- San Diego Ditch (canal)
- San Diego Reservoir (reservoir(s))
- Sandy Wash (stream)
- Sardella Lake (lake)
- Second Creek (stream)
- Second Garrotte (city)
- Shallow Lake (lake)
- Shamrock Lake (lake)
- Sharon Lake (lake)
- Shaws Flat (city)
- Shaws Flat Ditch (canal)
- Sheering Creek (stream)
- Shepherd Lake (lake)
- Shotgun Creek (stream)
- Sierra Village (city)
- Siesta Lake (lake)
- Silver Mine Creek (stream)
- Sister Lake (lake)
- Skelton Lakes (lake)
- Skull Creek (stream)
- Skunk Creek (stream)
- Slate Creek (stream)
- Smedberg Lake (lake)
- Smoothwire Creek (stream)
- Snow Lake (lake)
- Soap Creek (stream)
- Soldier Creek (stream)
- Soldier Lake (lake)
- Sonora (city)
- Sonora Creek (stream)
- Soulsbyville (city)
- Soulsbyville Ditch (canal)
- Sourgrass Lake (lake)
- South Fork (stream)
- South Fork Cathedral Creek (stream)
- South Fork Stanislaus River (stream)
- South Fork Stanislaus River (watercourse)
- South Fork Tuolumne River (stream)
- Spiller Creek (stream)
- Spiller Lake (lake)
- Spillway Lake (lake)
- Spotted Fawn Lake (lake)
- Spring Creek (stream)
- Standard (city)
- Stanislaus (city)
- Starvation Lake (lake)
- Stent (city)
- Strawberry (populated place)
- Sugarpine Creek (stream)
- Sullivan Creek (stream)
- Summit Lake (lake)
- Surprise Lake (lake)
- Swamp Lake (lake)
- Swamp Lake (lake)
- Sylvan Lodge (city)
- Table Lake (lake)
- Tallulah Lake (lake)
- Ten Lakes (lake)
- Thirteenmile Creek (stream)
- Thorps Creek (stream)
- Tilden Canyon Creek (stream)
- Tilden Creek (stream)
- Tilden Lake (lake)
- Tiltill Creek (stream)
- Toejam Lake (lake)
- Trout Creek (stream)
- Tunnel Creek (stream)
- Tuolumne City (city)
- Tuolumne Meadows (city)
- Turnback Creek (stream)
- Tuttletown (city)
- Twain Harte (city)
- Twain Harte Lake (Private) (lake)
- Twin Lakes (lake)
- Twin Meadows Lake (lake)
- Twomile Creek (stream)
- Unicorn Creek (stream)
- Upper Branigan Lake (lake)
- Upper Gaylor Lake (lake)
- Upper McCabe Lake (lake)
- Upper Peninsula Lake (lake)
- W Lake (lake)
- Waterhouse Lake (lake)
- West Fork Big Creek (stream)
- West Fork Cherry Creek (stream)
- Wheats Meadow Creek (stream)
- White Fir Creek (stream)
- White Wolf (city)
- Willow Creek (stream)
- Wilma Lake (lake)
- Wilson Creek (stream)
- Wire Lakes (lake)
- Wood Lake (lake)
- Woods Creek (stream)
- Woods Creek (stream)
- Wrights Creek (stream)