The Stonington Harbor Management Commission is a 10-member organization appointed by the Board of Selectmen and containing five Town and five Borough representatives serving two-year terms and the Harbor Master as ex-officio non-voting member.

The Commission is responsible for overseeing Stonington Harbor waters used for recreation, fishing, commercial and other uses; building of wharves, piers, and other structures at or in Stonington Harbor; anchoring or mooring of vessels; flow of waterborne traffic; access to Stonington Harbor waters; and management of the scenic, recreational, navigation, and fishing resources in Stonington Harbor. The Commission also develops and implements comprehensive plans, and coordinates with the Borough of Stonington, for the preservation, management, use, and development of Stonington Harbor waters.

The Stonington Shellfish Commission manages the important shellfish resources in Stonington Harbor and assures that these resources are carefully considered in harbor management activities undertaken by the Stonington Harbor Management Commission.

Stonington Harbor is 1.1 nautical miles from north to south and 4.4 nautical miles from east to west. Lying within the Town of Stonington, the harbor is separated from Lambert's Cove by a railroad causeway. Two railroad bridges serve the federal channel in Stonington Harbor. On the western shore, rock bluffs line Stonington Harbor. To the north are low beaches and small escarpments.

Being open to the south, ocean swells frequently cross the reefs to the east of Fishers Island and enter the harbor at high tide. Strong southern winds can push the waves to as much as 1.2 meters (4 feet).

Stonington Harbor is used by both commercial and recreational boaters. In addition to having the last commercial fishing fleet in Connecticut, Stonington Harbor is home base for some 400 recreational boats. It is a popular New England port for yachters and is a center for sailboat racing, motor boating, shore fishing, windsurfing, swimming, and scuba diving.

Stonington Harbor's Town Dock has two piers that extend from the east towards the channel. A off-loading facility for fish is located at the north main dock, which is 188 meters (618 feet) long. To the south of the main dock, the second Stonington Harbor pier is almost 138 meters (452 feet) long. Boats seek shelter from the waves by mooring in the water between the docks, and the north dock provides enough shelter for some vessels to berth there. Depths at the piers ranges from 2.1 to 4.6 meters (7 to 15 feet).

Stonington Harbor has about 400 permanent moorings, about 130 of them commercial moorings. During the summer boating season, as many as 300 boats visit Stonington Harbor, and groups of sailboats enter the harbor. Stonington Harbor provides transient anchorage in the harbor for these transient vessels.

Stonington Harbor has a full-service marina and boatyard that owns and services the commercial moorings and operates the only commercial moorings in the harbor. The boatyard provides transient and seasonal mooring rentals, a travel lift, fuel, pump out, and public toilets.

Just north of the railroad bridge is a small boat commercial marina and some individual moorings. Boaters can find small motorboat storage and tie-up and can rent outboard skiffs. Stonington Harbor also has twelve small boat launch ramps.

The Stonington Small Boat Association (SSBA) leases a storage area from the Town of Stonington. Located near the town launch ramp, recreational boats owned by town residents can be launched, hauled, and stored at this area. Some visiting cruise boats also use the area for dinghy landings.

Stonington Harbor contains a platform for recreational fishing at the west end of the North Wharf. To the south of the South Wharf is a public dinghy landing. Adjacent to the SSBA boat storage area is a small beach and boat launch. Stonington Harbor's Wayland Wharf has a temporary dinghy landing and small dock for recreational vessels.

Stonington Point is used by the public for recreational purposes that include parking, board sailing, scuba diving, and swimming. The public can pay a small fee to use DuBois Beach, a privately owned area.

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