The Village of Port Jefferson is the port authority for marine activities in Port Jefferson Harbor. The Port Jefferson Harbor Annex is home to the Harbormaster's Office and a marina offering ice and vending machines, showers, restrooms, a coin-operated laundry, a lounge and meeting room, and an outdoor picnic area. The Port Jefferson Harbor Launch Service offers transient moorings for vessels to 453 kilograms (1000 pounds) as well as anchorages. Customers have access to the Port Jefferson Harbor Annex's services and facilities.

The Port Jefferson Harbor Town Marina offers good shelter for boaters, and it is located just one block from the seaport village. Port Jefferson Harbor is a popular tourist destination, and the Town Marina is at its heart. The marina is open from May to November 1st. It offers 120 slips that can accommodate vessels to 13.7 meters (45 feet), including ten slips for transient boaters. The marina offers help with docking, dock carts, showers, toilets, a laundry, and pump-out service. While there is no boatyard at this Port Jefferson Harbor facility, engine, propeller, electric, and electronics repairs are available, as are bottom cleaning, wash and wax, and compound services.

The Port Jefferson Harbor's Setauket Yacht Club offers transient moorings to visitors. The Yacht Club has launch service, bathrooms and showers, ice, and water supply. Located next to PJ's Harborfront Park and the center of downtown Port Jefferson Harbor, the Yacht Club offers easy access to summer concerts, shops, restaurants, and other diversions.

Danford's Hotel & Marina offers 75 slips, all of which are open to transient vessels. The full-service hotel offers 86 guest rooms, a restaurant, and a fitness room. The secured marina can accommodate boats and yachts to 76 meters (250 feet). Marina amenities include bathrooms and showers, gas and diesel fuel, electrical hook-ups, water, cable TV, and high-speed wireless Internet. The Admiral's Deck offers New American al fresco dining and slip-side service. Danford's Hotel & Marina is located in the heart of Port Jefferson Harbor.

The Bridgeport and Port Jefferson Steamboat Company owns and operates the Port Jefferson Harbor Dock as a terminal for passenger and vehicle ferries moving between Port Jefferson Harbor and Bridgeport, Connecticut. The dock also offers mooring for idle ferries and tugboats and occasionally receives seafood. The Port Jefferson Harbor Dock has three berths. The first has berthing distance of 18.3 meters (60 feet) with alongside depth of with alongside depth of 6.1 meters (20 feet). The second and third berths have berthing distance of 85.3 meters (280 feet) with alongside depth of 6.1 meters (20 feet).

Northville-Consolidated Petroleum Terminal Inc. owns, and Miller Marine Services operates the Port Jefferson Harbor Mooring Dock where it moors service launches and oil spill, containment boom deployment, and line-handling vessels. Its two berths have berthing distance of 36.6 and 25.9 meters (120 and 85 feet) with alongside depth of three meters (10 feet).

Gotham Sand and Stone Corporation operates the Port Jefferson Harbor Aggregate Wharf owned by Port Dock & Stone Company and Laddie Acker. The Port Jefferson Harbor Aggregate Wharf is used to receive stone by barge, and it has an open storage area at the rear that can store 14 tons of stone. The wharf has berthing distance of 146.3 meters (480 feet) with alongside depth of 3.7 meters (12 feet).

Gotham Sand and Stone also owns and operates the Port Jefferson Harbor Tugboat Dock to moor tugboats. The Tugboat Dock has berthing distance of 15.2 meters (50 feet) with alongside depths of 2.4 and 0.6 meters (eight and two feet).

Keyspan Energy Inc. owns and operates the Port Jefferson Harbor Power Station Wharf to receive fuel oil for consumption by the power plant. Two pipelines connect the wharf to four storage tanks at the rear with capacity for 626 thousand barrels of fuel oil. There are about two acres of open storage at the rear of the wharf. The Port Jefferson Harbor Power Station Wharf has berthing distance of 219.5 meters (720 feet) with alongside depth of 8.8 meters (29 feet).

Tosco Pipeline Company operates the Port Jefferson Harbor Terminal Petroleum Dock owned by Northville-Consolidated Petroleum Terminal Inc. to ship and receive petroleum products. Flexible hoses on an adjustable rack connect pipelines that extend 5.6 kilometers (3.5 miles) to 30 steel storage tanks with capacity for 2.5 million barrels in East Setauket. The two berths at the Port Jefferson Harbor Terminal Petroleum Dock have berthing distance of 121.9 and 61 meters (400 and 200 feet) with alongside depths of 8.8 and 6.1 meters (29 and 20 feet), respectively.

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