| Arkansaw Creek |
| Big River |
| Brush Creek-Rush River |
| Burkhart Creek-Eau Galle Creek |
| Cady Creek |
| Cave Creek |
| City of Red Wing-Mississippi River |
| Crystal Springs Coulee-Rush River |
| Goose Creek-Trimbelle River |
| Isabelle Creek |
| Knights Creek |
| Lake Pepin |
| Little Trimbelle River |
| Lock and Dam No. 3-Mississippi River |
| Lost Creek |
| Lousy Creek-Eau Galle River |
| Lower Kinnickinnic Pond-Kinnickinnic River |
| Missouri Creek |
| Nugget Lake-Plum Creek |
| Parker Creek-Kinnickinnic River |
| Pine Creek |
| Porcupine Creek-Plum Creek |
| Saint Croix River |
| South Fork Kinnickinnic River |
| Spring Creek-Chippewa River |
| Spring Creek-Trimbelle River |
| Town of Martell-Ruh River |
| Township of Salem-Rush River |
| Trout Brook-Lake Saint Croix |
