Northeast Coastal Areas Study
Significant Coastal Habitats
Site 4 (NY)
I. SITE NAME: Port Jefferson - Stony Brook Harbor Complex
II. LOCATION: This area of protected harbors and adjacent uplands and wetlands is located along the north shore of central Long Island, in the vicinity of the villages of Port Jefferson and Stony Brook.
TOWNS: Brookhaven, Smithtown
COUNTY: Suffolk
STATE: New York
USGS 7.5 MIN QUADS: Port Jefferson, NY 40073-81;
Saint James, NY 40073-82
USGS 30x60 MIN QUAD: Long Island, West 40073-E1
II. GENERAL BOUNDARY: The boundary of this barrier beach and protected harbor complex, as delineated on the accompanying map, extends from Long Beach and the western shoreline of Stony Brook Harbor, between the Villages of Nissequogue and Stony Brook, along the coast in a northerly and then easterly direction to the eastern shoreline of Mt. Sinai Harbor, 1 mile (2 km) northeast of the Village of Port Jefferson. The individual embayment and beach units of significance to fish and wildlife within this complex are, from west to east: Long Beach, Stony Brook Harbor, West Meadow, Flax Pond, Old Field Beach, Conscience Bay, Little Bay, Setauket Harbor, Port Jefferson Harbor, McAllister County Park Beach, White Beach, and Mt. Sinai Harbor. The breadth of this complex, from southwest to northeast, is approximately 10 miles (16 km) across. The shoreward (inland) boundary is mostly confined to the immediate coastline and embayed areas and rarely extends more than 2 miles (3 km) inland, and this only in a few harbors.
IV. OWNERSHIP/PROTECTED STATUS: Most of the waters and wetlands are publicly-owned (State, County, Town) while ownership of some of the beach areas is mixed public and private property.
V. GENERAL HABITAT DESCRIPTION: The barrier beaches in this complex (Long Beach, West Meadow Beach, Flax Pond Beach, Old Field Beach, McAllister County Park Beach and White Beach) contain several undeveloped areas consisting of sparsely vegetated sand, gravel and cobble beaches and sand dunes along the shore of Long Island Sound, with some areas of dredging spoil deposits. Typical beach vegetation includes beachgrass (Ammophila breviligulata) and seaside goldenrod (Solidago sempervirens). Except for Port Jefferson Harbor, which ranges in depth from 6 to 30 feet (2-9 m), with a maximum of over 50 feet (15 m), most of the bays and harbors in this complex are shallow (less than 6 feet (2 m) in depth) and contain extensive tidal mudflats. Tidal fluctuation in these bays is approximately 7 feet (2 m). The shoreline of these bays varies from having fairly extensive tidal salt marshes, such as in Stony Brook Harbor, West Meadow, Mt. Sinai Harbor and Flax Pond, to heavy residential development, as in portions of Setauket Harbor.
VI. SIGNIFICANCE/UNIQUENESS OF AREA: The open waters of the harbors and bays of this complex are of regional significance as winter concentration areas and migration resting areas for waterfowl, particularly for several regional species of special emphasis such as American black duck (Anas rubripes), lesser and greater scaup (Aythya affinis and A. marila, respectively), mallard (Anas platyrhynchos), Canada goose (Branta canadensis), canvasback (Aythya valisineria), oldsquaw (Clangula hyemalis), bufflehead (Bucephala albeola), common goldeneye (Bucephala clangula), American wigeon (Anas americana) and red-breasted merganser (Mergus serrator). Waterfowl use of these bays and harbors in winter is influenced, in part, by the extent of ice cover in any given year. These embayments are also used for nesting by American black duck, Canada goose, green-backed heron (Butorides striatus), black-crowned night-heron (Nycticorax nycticorax), snowy egret (Egretta thula) and great egret (Casmerodius albus), with a major wading bird rookery located on the east end of Long Beach.
The waters of these areas are also extremely productive shellfish and finfish nursery and spawning areas, especially for winter flounder (Pseudopleuronectes americanus), bluefish (Pomatomus saltatrix), blackfish (Tautoga onitis), Atlantic silverside (Menidia menidia), hard-shelled clam (Mercenaria mercenaria), soft-shelled clam (Mya arenaria) and American oyster (Crassostrea virginica). There are indications that some of these bays may be used by juvenile Kemp's ridley (Lepidochelys kempii), a U.S. Endangered species and one of the rarest sea turtles, though the extent of use and significance of these areas to this and other sea turtle species is not well known.
The barrier beaches in this complex contain significant nesting colonies of piping plover (Charadrius melodus), a U.S. Threatened species, least terns (Sterna antillarum) and common terns (Sterna hirundo), although numbers are variable from year to year, probably due to disturbance during the nesting period. Flax Pond is the site of several important research studies and there is a New York State Department of Environmental Conservation research station at the site. In addition, the barrier beaches at Flax Pond and Old Field Beach are designated under the national Coastal Barrier Resources Act.
VII. THREATS: Residential and commercial marina development, including channel dredging and construction of shoreline structures, in the coastal watershed and harbors of this complex is of concern as regards water quality in these embayments. Fortunately, a considerable portion of the shoreline in these areas is relatively undeveloped and still contains substantial marsh and mudflat habitat and undeveloped woodlands on the upland margins. Beach habitats are under tremendous recreational pressure in this complex, resulting in human disturbances to nesting terns and piping plovers by boat-landings, picnicking, trampling of eggs and nests, and unleashed pets. In some cases this may have led to nest abandonment or reduced breeding success.
VIII. CONSERVATION CONSIDERATIONS: Improvement and protection of water quality in the embayments and nearshore waters should be given high-priority management focus to ensure the continued long-term value of this area for fish and wildlife populations of regional importance, particularly for wintering waterfowl, shellfish beds, spawning and juvenile finfish, and colonial beach-nesting birds. Disturbances by humans and pets to beach-nesting colonial birds and wading bird rookeries is of major concern and should be prevented. Methods to be applied include protective fencing and exclosures, posting, warden patrols, predator/pet removal and public education. Efforts should be made to implement objectives and tasks outlined in the piping plover recovery plan that may be applicable to beaches in this complex, including habitat improvement and enhancement actions. Cooperative management and conservation agreements may need to be developed among the various governmental agencies and landowners to protect not only beach nesting areas, but marsh nesting species and wintering waterfowl concentrations. Opportunities should also be sought to enhance wetland habitats in support of the North American Waterfowl Management Plan-Atlantic Coast Joint Venture.
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