The main harbor of the Port of Thorne Bay is located on the bay's north side, where most of the town's retail businesses are located. Harbor amenities include fresh water, public showers and restrooms, some electricity, and a fish cleaning station. Dry dock is available at a fee for boat maintenance and repairs. There is also float plane moorage in the Port of Thorne Bay harbor.

The Small Boat Harbor Floats in the Port of Thorne Bay are owned jointly by the State of Alaska and the City of Throne Bay. The State of Alaska's Department of Transportation and Public Facilities operates the floats, which provide mooring for commercial and recreational vessels and landing for seaplanes. The main float has 5.2- to 6.4-meter (17- to 21-foot) stalls. The Port of Thorne Bay's Small Boat Harbor Floats have alongside depth of 4.9 meters (16 feet) MLLW.

There is a launch ramp at the north side of the floats. At the end of Float B is a 22.9- by 12.2-meter (75- by 40-foot) float used for landing of seaplanes. The State of Alaska owns, and the City of Thorne Bay operates, the Seaplane Float which offers 100.6 meters (330 feet) of berthing distance with alongside depth of 4.9 meters (16 feet) MLLW.

Boyer Towing, Inc. owns, and the Boyer Alaska Barge Line, Inc. and Petro Alaska, Inc. operate the Thorne Bay Transfer Bridge. This Port of Thorne Bay wharf handles conventional and containerized general cargo and receives petroleum products. Located at the north side of Thorne Bay at Sandy Beach Road, there as an about 3.5-acre open storage area at the rear of the wharf. Petro Alaska has two pipelines that connect the wharf to 12 steel storage takes with total capacity for 6500 barrels. The Port of Thorne Bay Transfer Bridge has berthing distance of 61 meters (200 feet) with alongside depth of 3 meters (10 feet) MLLW.

The Tackle Shack, Port of Thorne Bay Fuel Float is owned by the City of Thorne Bay and operated by the Tackle Shack to fuel small vessels. Located on the north side of Thorne Bay on Freeman Drive, the Fuel Float is connected ashore by one fueling pipeline to a steel storage tank with capacity for 70 barrels. The Port of Thorne Bay Tackle Shack Fuel Float has berthing distance of 30.5 meters (100 feet) with alongside depth of 3 meters (10 feet) MLLW.

The Port of Thorne Bay owns and operates the Thorne Bay Fuel Float located on Sandy Beach Road. The Port of Thorne Bay Fuel Float is used to fuel small vessels and for seaplane landing. The wharf is connected to two steel storage tanks with total capacity of 70 barrels by two fueling pipelines. The Port of Thorne Bay Fuel Float has berthing distance of 36.6 meters (120 feet) with alongside depth of 3 meters (10 feet) MLLW.

While it is not currently in use, the Ketchikan Pulp Company's Thorne Bay Dock is located on the northwest side of Thorne Bay. Log ponds have capacity for about 20 million board feet of logs, and an open storage area at the rear of the wharf has capacity for about four million board feet. Once used to receive and ship logs, this Port of Thorne Bay Dock has berthing distance of 21.3 meters (70 feet) with alongside depth of 3 meters (10 feet).

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