| Allen Creek |
| Amherst Island-Frontal Lake Ontario |
| Angelica Creek |
| Baker Creek |
| Bald Eagle Creek |
| Beards Creek |
| Bebee Creek-Honeoye Creek |
| Bennett Creek-Canaseraga Creek |
| Black Creek |
| Black Creek-Angelica Creek |
| Black Creek-Genesee River |
| Bradner Creek |
| Brighton Cliff-Frontal Lake Ontario |
| Brimmer Brook-Genesee River |
| Brockport Creek-Otis Creek |
| Browns Creek-Genesee River |
| Buttonwood Creek-Frontal Braddock Bay |
| Canadice Lake-Outlet Canadice Lake |
| Canaseraga Creek |
| Caneadea Creek |
| Chenunda Creek |
| Christie Creek-Genesee River |
| City of Le Roy-Oatka Creek |
| Cold Creek |
| Cowsucker Creek-Frontal Lake Ontario |
| Crawford Creek-Genesee River |
| Cryder Creek |
| Dugan Creek-Genesee River |
| Durand Lakes |
| East Branch Sandy Creek-Sandy Creek |
| East Koy Creek |
| Eastover Brook-Genesee River |
| Ford Brook-Genesee River |
| Fourmile Creek |
|
| Genesee River |
| Gordon Brook-Genesee River |
| Hamlet of Portageville-Genesee River |
| Headwaters Black Creek |
| Headwaters Canaseraga Creek |
| Headwaters Caneadea Creek |
| Headwaters East Koy Creek |
| Headwaters Genesee River |
| Headwaters Irondequoit Creek |
| Headwaters Keshequa Creek |
| Headwaters Oatka Creek |
| Headwaters Wiscoy Creek |
| Hemlock Lake |
|
| Honeoye Creek |
| Honeoye Inlet |
| Honeoye Lake-Honeoye Creek |
| Hotel Creek-Black Creek |
| Irondequoit Bay |
|
| Irondequoit Creek |
| Jaycox Creek-Genesee River |
| Keshequa Creek |
| Knight Creek |
| Lake Ontario |
| Larkin Creek |
|
| Little Black Creek |
| Lower Conesus Creek |
| Lower Dyke Creek |
| Marsh Creek |
| Marsh Creek-Genesee River |
| Middle Branch Genesee River |
| Middle Conesus Creek |
| Middle Dyke Creek |
|
| Mill Creek |
| Mill Creek-Black Creek |
| Mill Creek-Frontal Lake Ontario |
| Moorman Creek |
| Mud Creek |
| Mud Creek-Canaseraga Creek |
| Northrup Creek |
|
| Oatka Creek |
| Outlet Hemlock Lake |
| Outlet Silver Lake-Genesee River |
| Pearl Creek-Oakta Creek |
| Phillips Creek |
|
| Red Creek |
| Robins Brook-Black Creek |
| Round Pond Creek |
| Rush Creek |
|
| Salmon Creek |
|
| Sandy Creek |
| Shongo Creek-Genesee River |
| Silver Lake |
| Slater Creek-Frontal Lake Ontario |
| Spring Brook-Honeoye Creek |
| Spring Creek |
| Stony Brook-Canaseraga Creek |
| Sugar Creek |
| Thomas Creek-Irondequoit Creek |
| Town of Gates-Genesee River |
| Trout Brook |
| Twomile Creek |
| Upper Conesus Creek |
| Upper Dyke Creek |
| Van Campen Creek |
| Vandermark Creek |
| Village of Fillmore-Genesee River |
| West Branch Genesee River |
| West Branch Van Campen Creek |
| West Creek |
| White Creek-Genesee River |
| White Creek-Oatka Creek |
| Wiscoy Creek |
| Wolf Creek-Genesee River |
|
| Yanty Creek |
