| Armand Bayou |
| Arroyo Colorado |
| Attoyac Bayou |
| Barton Springs and Onion Creek |
| Bastrop Bayou |
| Brady Creek |
| Buck Creek |
| Caddo Lake |
| Cedar Bayou |
| Cedar Creek Reservoir |
| Concho River |
| Cypress Creek |
| Dickinson Bayou |
| Double Bayou |
| Eagle Mountain Reservoir |
| Geronimo and Alligator Creeks |
| Hickory Creek |
| Lake Arlington |
| Lake Granbury |
| Lake Granger |
| Lampasas River |
| Leon River |
| Lower Nueces River |
| Moses-Highland-Karankawa Bayous |
| Paso del Norte de Rio Grande |
| Pecos River |
| Plum Creek |
| San Bernard River |
| San Felipe Creek |
| South and North Llano Rivers |
| Upper Cibolo Creek |
| Upper San Antonio River |
| Upper San Marcos River |