| Name | County(ies) |
| Alligator Lake | Columbia |
| Ansin/Garcia Miami Lakes | Indian River |
| Apalachicola River | Gulf, Liberty, Franklin, Jackson, Gadsden, Calhoun |
| Blackwater and Yellow Rivers | |
| Lake Blue Cypress | Indian River |
| Chipola River | Calhoun |
| Choctawhatchee River | |
| Clermont Chain | Lake |
| Lake Crescent | Flagler, Putnam |
| Dead Lake | Calhoun, Gulf |
| Deerpoint Lake | Bay |
| Doctors Inlet | Clay |
| Emeralda Marsh | Lake |
| Escambia River | |
| Everglades Conservation Areas | Palm Beach, Broward, Dade |
| Farm-13/Stick Marsh | Indian River |
| Lake George | Putnam, Volusia |
| Hamilton Cnty Phosp. Pits | Hamilton |
| Lake Harris | Lake |
| Hurricane Lake | Okaloosa |
| Lake Istokpoga | Highlands |
| Lake Jackson | Leon |
| Kenansville Lake | Indian River |
| Lake Kissimmee | Osceola |
| Lake Lochloosa | Alachua |
| Medard Reservoir | Hillsborough |
| Merritt's Mill Pond | |
| Miami-Dade, Broward & West Palm Canals | Broward, Miami-Dade, West Palm |
| Lake Monroe | Seminole, Volusia |
| Newnan's Lake | Alachua |
| Ocala Forest Lakes | Lake, Marion |
| Ocheesee Pond | |
| Ochlockonee River | |
| Okeechobee | Palm Beach, Martin, Glades, Okeechobee, Hendry |
| Oklawaha River | Marion, Putnam |
| Orange Lake | Alachua |
| Lake Osborne | Palm Beach |
| Lake Panasoffkee | Sumter |
| Lake Parker | Polk |
| Peace River | Polk, Hardee, Desoto, Charlotte |
| Rodman Reservoir | Putnam |
| Lake Rousseau | Citrus and Levy |
| Saddle Creek Park | Polk |
| St. Johns River | Brevard, Flagler, Lake, Orange, Putnam, Seminole, St. Johns, Volusia |
| St. Mary's River | |
| Lake Sampson | Bradford |
| Lake Santa Fe | Alachua |
| Lake Seminole | Jackson, Gadsden |
| Suwannee Lake | Suwannee |
| Suwannee/Santa Fe Rivers | Suwannee, et al. |
| Lake Talquin | Gadsden, Leon |
| Lake Tarpon | Pinellas |
| Tenoroc Pits | Polk |
| Lake Tohopekaliga | Osceola |
| Lake Trafford | Collier |
| Tsala Apopka Chain | Citrus |
| Lake Victor | Holmes |
| Lake Walk-in-Water | Polk |
| Wauberg Lake | Alachua |
| Webb Lake & Marl Ponds | Polk |
| Winter Haven Chain | Polk |
| Withlacoochee River | Citrus, Marion, Sumter, Levy, Hernando |
| Withlacoochee River | |
| Lake Yale | Lake |
