| Santa Fe River | Gilchrist, FL | 10.1 miles | NW |
| Cow Creek | Gilchrist, FL | 10.6 miles | NE |
| Brushy Creek | Dixie, FL | 12.6 miles | SW |
| Ichetucknee River | Suwannee, FL | 13.3 miles | NE |
| Hammock Branch | Columbia, FL | 19.4 miles | NE |
| Pareners Branch | Alachua, FL | 20.6 miles | NE |
| Townsend Branch | Alachua, FL | 21.3 miles | NE |
| Olustee Creek | Union, FL | 23.5 miles | NE |
| Mill Creek | Alachua, FL | 24.1 miles | NE |
| Rose Creek | Columbia, FL | 24.2 miles | NE |
| Little River | Suwannee, FL | 24.4 miles | NW |
| Turkey Creek | Alachua, FL | 24.6 miles | NE |
| Blues Creek | Alachua, FL | 24.7 miles | SE |
| Wolf Creek | Lafayette, FL | 25.3 miles | NW |
| Cedar Branch | Levy, FL | 25.9 miles | SW |
| Week Creek | Dixie, FL | 26.2 miles | SW |
| Fishbone Creek | Dixie, FL | 26.7 miles | SW |
| Swift Creek | Union, FL | 27.4 miles | NE |
| Swift Creek | Union, FL | 27.4 miles | NE |
| Mud Creek | Lafayette, FL | 27.5 miles | NW |
| Clay Hole Creek | Columbia, FL | 27.6 miles | NE |
| Cannon Creek | Columbia, FL | 27.8 miles | NE |
| Crossway Branch | Lafayette, FL | 27.8 miles | NW |
| Owl Creek | Lafayette, FL | 27.8 miles | NW |
| Calf Creek | Lafayette, FL | 27.9 miles | NW |
| Eightmile Creek | Dixie, FL | 28.1 miles | NW |
| Kettle Creek | Lafayette, FL | 28.2 miles | NW |
| Rose Creek | Columbia, FL | 28.2 miles | NE |
| Twomile Branch | Lafayette, FL | 28.4 miles | NW |
| Alligator Branch | Lafayette, FL | 28.5 miles | NW |
| New River | Union, FL | 28.7 miles | NE |
| California Creek | Dixie, FL | 28.8 miles | SW |
| Hogtown Creek | Alachua, FL | 29.3 miles | SE |
| Rocky Creek | Taylor, FL | 29.7 miles | SW |
| Turkey Creek | Dixie, FL | 29.8 miles | SW |
| Boggy Creek | Taylor, FL | 29.9 miles | SW |
| Crab Creek | Suwannee, FL | 29.9 miles | NW |
| Lilly Creek | Dixie, FL | 30 miles | SW |
| Rocky Creek | Bradford, FL | 30 miles | NE |
| Boat Creek | Dixie, FL | 30.5 miles | SW |
| Magee Branch | Levy, FL | 30.5 miles | SE |
| Britt Creek | Lafayette, FL | 30.6 miles | NW |
| Flag Creek | Dixie, FL | 30.9 miles | SW |
| Little Britt Creek | Lafayette, FL | 31.1 miles | NW |
| Sand Hill Creek | Dixie, FL | 31.2 miles | SW |
| Sandfly Creek | Levy, FL | 31.2 miles | SW |
| Amason Creek | Dixie, FL | 31.6 miles | SW |
| Fishbone Creek | Dixie, FL | 31.6 miles | SW |
| Reedy Creek | Lafayette, FL | 31.6 miles | NW |
| Butler Creek | Dixie, FL | 31.7 miles | SW |
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