As it is on an isolated island, the Port of St. Paul can be reached only by air and sea. The State of Alaska owns an almost two thousand meter (6500-foot) asphalt runway, but most freight and supplies are carried to the Port of St. Paul by ship. In addition to the existing breakwater with 213 meters (700 feet) of dock space and a barge off-loading area, the Port of St. Paul began to build a small boat harbor in 2009 that has stimulated economic growth.

The Port of St. Paul supports the Central Bering Sea fishing fleet. Thirty residents of the Port of St. Paul have commercial fishing permits for halibut. In 1981, Trident Seafoods built a crab-processing plant in the Port of St. Paul. More recently, cold storage facilities have been added. Today, Icicle and Unisea fish processors have facilities near the harbor, and as many as nine off-shore processors make the Port of St. Paul their base.

Pilotage is required for all but a few exempted vessels. Alaska Marine Pilots provide services in the Bering Sea. The normal anchorage at the Port of St. Paul is west of Village Cove between Reef Point and Zapadni Point. Anchorage can also be found northeast of Reef Point in Lukanin off Bay off Black Buffs and East Landing.

When the ice edge begins to move to the north in April and May, the Port of St. Paul is dramatically affected by the winds. Vessels should not try to ride out gales while anchored near the islands. They should also faithfully watch for ice to avoid becoming trapped.

The harbor at the Port of St. Paul is a shelter for the Baltic Sea fishing fleet. In 2006, the entrance channel depth was 5.5 meters (18 feet). The Port of St. Paul has three main docks with deck heights of 3.4 meters (11 feet) and alongside depths from 2.9 to 7 meters (9.5 to 23 feet). Vessels are advised to keep close to the shore, as the harbor becomes shallow rapidly in the northeast. Vessels are also advised that heavy swells may also be a problem near the entrance to the Port of St. Paul. Vessels may not land at the fur seal rookeries during the breeding season from early June to mid-October.

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