As Kauai's second commercial harbor, after Nawiliwili Harbor, Port Allen Harbor has facilities for the movement of liquid bulk cargoes (mainly petroleum). It is also used to moor excursion, charter, and military vessels.

The State of Hawaii's Harbors Division within the Department of Transportation manages Port Allen Harbor. The Harbors Division is responsible for planning, designing, building, operating, and maintaining State water transportation facilities. The Harbors Division also coordinates with other government programs and agencies to assure the efficient and effective operation of Hawaii's commercial harbors. At present, the Harbors Division manages ten commercial harbors, including Port Allen Harbor.

The Harbors Division owns and operates the Port Allen Harbor Pier. The Pier is used to receive petroleum products, fuel oil, and liquid fertilizer as well as for mooring vessels. The Pier has berthing space of 38 meters (124 feet) with alongside depth of almost 11 meters (35 feet) MLLW.

Chevron Products Company operates two pipelines that connect the Port Allen Harbor Pier to nine storage tanks with total capacity for more than 108 thousand barrels at the rear of the pier. The Gas Company (Citizens Utilities Company) has a pipeline that moves fuel oil from the pier to the company's Port Allen Station. Brewer Environmental Industries has a pipeline from the wharf to a 630-thousand-gallon storage tank for liquid fertilizer.

The United States' Pacific Missile Range Facility and Naval Undersea Warfare Engineering Station lease about 2.4 thousand square meters (25.5 thousand square feet) of space in the transit shed behind the Port Allen Harbor Pier.

The Port Allen Harbor Small Boat Harbor is located some 122 meters (400 feet) north of the Port Allen Harbor Pier. The Small Boat Harbor has six moorings with 34 berths. It offers a two-lane 9-meter (30-foot) wide launch ramp and a loading dock. The harbor office and public restrooms are located here. The Small Boat Harbor also has a fish hoist and offers vessel wash-down services.

Kauai island has five capital improvement projects underway to improve the island's recreational infrastructure. One of these projects is to make ocean recreation improvements in Port Allen Harbor. The project includes maintenance dredging as well as making improvements to the boat ramp, the loading dock, the comfort station, roads, and parking areas.

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