| Beards Creek-Genesee River |
| Big Stream-Seneca Lake |
| Black Creek |
| Canadaigua Lake |
| Cayuga Inlet |
| Conesus Creek |
| Flint Creek |
| Fourmile Creek-Frontal Lake Ontario |
| Ganargua Creek-Erie Canal |
| Genesee River |
| Headwaters Honeoye Creek |
| Honeoye Creek |
| Irondequoit Creek-Frontal Lake Ontario |
| Keuka Lake |
| Lower Chemung River |
| Lower Cohocton River |
| Lower Seneca River |
| Middle Chemung River |
| Middle Cohocton River |
| Middle Seneca River |
| Mud Creek |
| Ninemile Creek-Frontal Lake Ontario |
| Oakta Creek |
| Oatka Creek |
| Onondaga |
| Outlet Canadaigua Lake |
| Owasco Lake |
| Salmon Creek-Cayuga Lake |
| Salmon Creek-Frontal Lake Ontario |
| Seneca Lake Inlet |
| Sodus Bay |
| Sterling Creek-Frontal Lake Ontario |
| Upper Chemung River |
| Upper Cohocton River |
| Upper Seneca River |
| Wolcott Creek-Frontal Lake Ontario |
| Yawger Creek-Cayuga Lake |