The Port of Metlakatla is a private company that employs as many as four people.

The City of Metlakatla owns and operates the Port of Metlakatla City Dock which serves for mooring of cruise ships. Located in Port Chester Bay about 610 meters (2000 feet) southeast of Village Point in the Port of Metlakatla, the City Dock offers berthing space of 122 meters (400 feet) with alongside depth of 10.6 meters (35 feet).

The City also owns the Port of Metlakatla's City Barge Ramp, which is operated by the Alaska Barge Line, Inc. The Barge Ramp receives and ships containerized and roll-on/roll-off cargo. There is an unpaved open storage area at the rear of the ramp with capacity for about 400 containers. Located in Port Chester Bay about 640 meters (2100 feet) southeast of Village Point in the Port of Metlakatla, the City Barge Ramp has 122 meters (400 feet) of berthing space with alongside depth of 4.5 meters (15 feet).

The Port of Metlakatla Seaplane Float is owned by the State of Alaska and operated by the City. Located in Port Chester Bay about 106 meters (350 feet) southeast of Village Point in the Port of Metlakatla, seaplanes land at the Float which also has a paved parking lot. The Seaplane Float has berthing distance of 46 meters (150 feet) with alongside depth of 3 meters (10 feet).

The city-owned Port of Metlakatla City Wharf has been used as a private seaplane float; however, it is not always in use. Located on Port Chester Bay on the west side of the Port of Metlakatla's Village Point, the City Wharf has berthing distance of 24 meters (80 feet) with alongside depth of 3 meters (10 feet).

The State-owned Port of Metlakatla Old Harbor Floats is operated by the City for mooring of commercial and recreational vessels. A 274-meter (900-foot) stone breakwater forms the basin where Float 2 contains eight 7.3-meter (24-foot) stall floats. The harbor can berth about 48 vessels, and it has a 61- by 3.6-meter (200- by 12-foot) concrete launching ramp. Located at the foot of Eighth Avenue in the Port of Metlakatla, the Old Harbor Floats offer 208 meters (684 feet) of berthing space with alongside depth of 3 meters (10 feet).

The Annette Island Packing Company operates the city-owned Metlakatla Wharf to receive seafood and ice fishing vessels. A seafood processing plant and cold storage facility are located at the wharf. There is a 12-inch pipeline for unloading seafood and a 6-inch line for icing vessels at the wharf. Also located in Port Chester Bay about 305 meters (1000 feet) southeast of the Port of Metlakatla's Village Point, the Metlakatla Wharf has 84 meters (275 feet) of berthing space with alongside depth of 7 meters (23 feet).

The Port of Metlakatla also contains a fuel transfer dock for receiving barges carrying petroleum products and the State of Alaska's Metlakatla Ferry Terminal Dock for serving passenger and vehicular traffic.

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