| Alafia River | 24.7 | 74 |
| Alafia River - North Prong | 21.8 | 22 |
| Alafia River - South Prong | 27.9 | 28 |
| Alapaha River | 23.2 | 25 |
| Alapahoochee River | 1.8 | 2 |
| Alaqua Creek | 32.6 | 33 |
| Alligator Creek | 13.1 | 13 |
| Anclote River | 29.1 | 29 |
| Apalachicola River | 109.2 | 399 |
| Attapulgus Creek | 7.5 | 12 |
| Aucilla River | 60.2 | 93 |
| Bear Creek | 29.9 | 43 |
| Big Coldwater Creek | 11.1 | 57 |
| Big Coldwater Creek - East Fork | 20.7 | 21 |
| Big Coldwater Creek - West Fork | 25.3 | 25 |
| Big Escambia Creek | 4.3 | 4 |
| Big Juniper Creek | 28 | 46 |
| Black Creek (Gulf of Mexico tributary) | 18.9 | 19 |
| Black Creek - North Fork (St. Johns River tributary) | 32.2 | 32 |
| Black Creek - South Fork (St. Johns River tributary) | 22.9 | 23 |
| Black Creek (St. Johns River tributary) | 14.5 | 82 |
| Black Water Creek | 19.7 | 20 |
| Blackwater River (Gulf of Mexico tributary) | 51.6 | 179 |
| Blue Creek | 11.9 | 12 |
| Braden River | 22.6 | 23 |
| Broad River | 17.6 | 29 |
| Brothers River | 15.4 | 15 |
| Bruce Creek | 25.7 | 26 |
| Brushy Creek (Perdido River tributary) | 17 | 17 |
| Bull Creek | 25.3 | 25 |
| Bullfrog Creek | 19.2 | 19 |
| Caloosahatchee Canal | 15.7 | 16 |
| Caloosahatchee River | 55.1 | 82 |
| Canoe Creek | 13.1 | 13 |
| Cedar Creek | 13 | 13 |
| Charlie Creek | 41.9 | 61 |
| Chattahoochee River | 25 | 25 |
| Chipola River | 92.5 | 192 |
| Choctawhatchee River | 91.8 | 326 |
| Cowarts Creek | 8.4 | 8 |
| Cow Creek | 16 | 34 |
| Crabgrass Creek | 11.1 | 11 |
| Crooked River | 26.1 | 26 |
| Dry Creek | 14.8 | 15 |
| East Bay River | 18.1 | 31 |
| Ecofina Creek | 44.7 | 88 |
| Ecofina River | 43.9 | 44 |
| Econlockhatchee River | 43.7 | 60 |
| Eightmile Creek | 12.6 | 13 |
| Escambia River | 58.9 | 105 |
| Etonia Creek | 16.1 | 30 |
| Falling Creek | 18.1 | 18 |
| Fenholloway River | 38.6 | 71 |
| Fisheating Creek | 73.7 | 74 |
| Flat Creek | 14.3 | 14 |
| Fourmile Creek (Chipola River tributary) | 20.7 | 21 |
| Fourmile Creek (Gulf of Mexico tributary) | 8.8 | 22 |
| Gamble Creek | 19.6 | 20 |
| Gum Creek | 17 | 17 |
| Hard Labor Creek | 16.6 | 17 |
| Hillsborough River | 53.1 | 64 |
| Holmes Creek | 61.5 | 91 |
| Horse Creek | 53.9 | 54 |
| Horsehead Creek | 11.8 | 12 |
| Jane Green Creek | 9.2 | 46 |
| Jim Creek | 14.3 | 14 |
| Joshua Creek | 24.7 | 25 |
| Jumper Creek | 23.6 | 24 |
| Juniper Creek | 29.9 | 30 |
| Kennedy Creek | 18.6 | 19 |
| Lafayette Creek | 13.6 | 14 |
| Little Aucilla River | 19.8 | 20 |
| Little Bear Creek | 13.1 | 13 |
| Little Charlie Creek | 14.2 | 14 |
| Little Econlockhatchee River | 16.5 | 17 |
| Little Escambia Creek | 0.3 | 0 |
| Little Manatee River | 37.3 | 56 |
| Little Manatee River - South Fork | 18.9 | 19 |
| Little River | 15.5 | 48 |
| Little St. Marys River | 18.5 | 19 |
| Little Suwannee Creek | 8.9 | 9 |
| Little Withlachooche River | 21.1 | 21 |
| Live Oak Creek | 12.6 | 13 |
| Manatee River | 36.3 | 106 |
| Manatee River - East Fork | 13.6 | 14 |
| Manatee River - North Fork | 14.2 | 14 |
| Marshall Creek | 9 | 9 |
| Mosquito Creek | 4.2 | 25 |
| Myakka River | 71.3 | 82 |
| New River (Gulf of Mexico tributary) | 55.9 | 56 |
| New River (Santa Fe River tributary) | 30.5 | 31 |
| North Mosquito Creek | 7 | 7 |
| Oak Creek (Charlie Creek tributary) | 18.7 | 19 |
| Oak Creek (Peace River tributary) | 14.8 | 15 |
| Ochlockonee River | 119.7 | 265 |
| Ocklawaha River | 77.1 | 89 |
| Olustee Creek | 28.2 | 41 |
| Orange Creek | 11.9 | 12 |
| Owen Creek | 10.3 | 10 |
| Peace Creek | 15.3 | 15 |
| Peace River | 109.1 | 333 |
| Perdido River | 63.4 | 80 |
| Peters Creek | 12 | 12 |
| Pine Barren Creek (Escambia River tributary) | 27.9 | 28 |
| Pithlachascotee River | 22.6 | 23 |
| Pond Creek (Blackwater River tributary) | 24.7 | 25 |
| Pond Creek (Shoal River tributary) | 19.8 | 32 |
| Prairie Creek | 18.7 | 19 |
| Quincy Creek | 11.2 | 11 |
| Rice Creek | 16.3 | 46 |
| Rocky Creek (Gulf of Mexico tributary) | 22.6 | 23 |
| Rocky Creek (Spring Creek tributary) | 15.7 | 16 |
| Sandy Creek | 33 | 45 |
| Sandy Creek | 14.6 | 15 |
| Santa Fe River | 80.5 | 152 |
| Seven Runs | 15.8 | 16 |
| Shell Creek | 22.1 | 41 |
| Shoal River | 44.1 | 116 |
| Simms Creek | 13.5 | 14 |
| Sopchoppy River | 39.6 | 40 |
| South Mosquito Creek | 13.3 | 13 |
| Spring Creek | 16.4 | 32 |
| Spring Run | 12.8 | 13 |
| Spring Warrior Creek | 13.1 | 13 |
| Steinhatchee River | 34.5 | 35 |
| St. Johns River | 278.7 | 671 |
| St. Marks River | 39.3 | 51 |
| St. Marys River | 125.4 | 223 |
| St. Marys River - Middle Prong | 19.6 | 20 |
| St. Marys River - North Prong | 14.3 | 14 |
| St. Marys River - South Prong | 31.9 | 32 |
| Suwannee River | 208 | 440 |
| Swamp Creek | 4.5 | 5 |
| Sweetwater Creek (Big Juniper Creek tributary) | 17.7 | 18 |
| Swift Creek | 12.9 | 13 |
| Telogia Creek | 71.6 | 72 |
| Tenmile Creek (Chipola River tributary) | 16.7 | 17 |
| Tenmile Creek (Cow Creek tributary) | 17.8 | 18 |
| Tenmile Creek (Wrights Creek tributary) | 14.6 | 15 |
| Titi Creek | 23.5 | 24 |
| Trout Creek (Caloosahatchee River tributary) | 10.9 | 11 |
| Trout Creek (Hillsborough River tributary) | 10.6 | 11 |
| Trout River | 19.5 | 20 |
| Waccasassa River | 26.4 | 26 |
| Wacissa River | 12.8 | 13 |
| Wakulla River | 11.4 | 11 |
| Wekiva River | 16.1 | 36 |
| Wetappo Creek | 25.3 | 25 |
| Willacoochee Creek (Little River tributary) | 9.1 | 9 |
| Withlachooche River | 140.8 | 186 |
| Withlacoochee River | 28.2 | 28 |
| Wood River | 11 | 11 |
| Wrights Creek | 29.3 | 44 |
| Yellow River | 67.8 | 184 |
