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Town of Shelter Island |
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| Water Body Name | Historic Eelgrass | Current Eelgrass | Last Recorded |
| Bass Creek | ND | N | ND |
| Cedar Island Cove | Y | N | ND |
| Chase Creek | ND | N | ND |
| Coecles Harbor | Y | Y | 2010 |
| Congdons Creek | Y | N* | 2000 |
| Crab Creek | Y | N | ND |
| Dering Harbor | Y | N | 1960's |
| Dickerson Creek | ND | N | ND |
| Foxen Creek | Y | N | Early 2000's* |
| Gardiners Bay (Entirety) | Y | Y | 2010 |
| Gardiners Bay-Cornelius Point | Y | N* | 2008 |
| Gardiners Bay-Hay Beach | Y | Y | 2010 |
| Gardiners Bay-Little Ram Island | Y | Y | 2010 |
| Gardiners Bay-Ram Island | Y | Y | 2010 |
| Gardiners Creek | Y | N | 1940's |
| Majors Harbor | Y | N* | ND |
| Menatic Creek | Y | N | ND |
| Nicoll's/Miss Annie Creek | Y | N* | 2006* |
| Nicoll Point | Y | Y | 2008 |
| Shanty Bay | Y | N | ND |
| Shelter Island Sound-North of Crab Creek | Y | N | 1960's |
| Shelter Island Sound-West Neck Area | Y | N | 1960's |
| Smith Cove | N | N | |
| West Neck Bay | Y | N | ND |
| West Neck Creek | Y | N | ND |
| West Neck Harbor | Y | N | ND |
| Unk. Creek (Next to Ms. Annies) | Y | N* | ND |
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