Acabonack Harbor is located midway on the South Fork of Long Island along the shore of Gardiners Bay and southwest of Gardiners Island. The Acabonack Harbor is a habitat complex of shallow open water (less than 6 feet (2 m) deep), extensive tidal salt marshes dominated by cordgrasses (Spartina alterniflora and S. patens), mud flats, spoil disposal areas, and small wooded islands. The landward areas around the harbor and marshlands are mostly undeveloped woodlands. East of the enclosed water and marsh system is a barrier spit system that serves as the primary boundary between the harbor and Gardiners Bay. This sandy and pebbly beach and dune complex is sparsely to moderately vegetated and in some areas contains dredging spoils. Lionhead Beach and Sammys Beach provide similar habitat. The Acabonack Harbor area serves as an important feeding area for osprey (Pandion haliaetus) - both for birds nesting in the area as well as those which nest on Gardiners Island, 4 miles (6 km) to the northeast. Acabonack Harbor, just west of Cartwright Island, has a narrow channel with privately maintained markers. The channel is 2.5 feet deep, but there is more water inside.
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