Mt. Sinai Harbor is located approximately one mile northeast of the Village of Port Jefferson, on the north shore of Long Island. This approximate 400 acre area is located in the Town of Brookhaven, Suffolk County. The fish and wildlife habitat consists of salt marsh, mudflats, and open water area in the bay, excluding the area along the western part of Cedar Beach which is developed as a marina and boat mooring area. The entire area is owned by the Town of Brookhaven for conservation purposes. The bay is bordered by low density residential development and undeveloped woodlands.

The mooring field in Mount Sinai Harbor can accomodate 500 boats and annual permits are controlled by the Town of Brookhaven. Boat slips are available in the town marina, Old Man's Boat Yard, Mount Sinai Yacht Cub and Ralph's Fishing Station. There are currently waiting lists for boat slips and you should contact each for more information.

During the summer months, pump-out boats are operated by the Town for use by boaters in our waterways, at no charge. Currently, these boats are located on the North Shore in both the Port Jefferson and Mount Sinai Harbors. In order to contact the pump out boats, you may use channel 71 or simply wave them down as they patrol the local marina. These boats primarily function Friday thru Sunday, as well as on holidays. For all other pump-out needs, please visit one of out 24-hour self-serve stations. The self-serve stations can be found in the Mount Sinai harbor, located just East of Old Mans Boat Yard.