Wellfleet Harbor is located on the east side of Cape Cod Bay in Wellfleet, about 12 miles south of Provincetown Harbor. It is an active center for recreational boating, commercial fishing, and sport fishing charter boats.

The earliest work in the harbor, completed in 1899, consisted of a channel four feet deep extending from deep water to the town wharves at Duck Creek at the head of the harbor. In 1916, the state dredged the channel to a depth of six feet.

In 1958, the Corps completed modifications to Wellfleet Harbor. These included dredging an 0.8-mile-long channel, 10 feet deep and 125 feet wide, extending from "Deep Hole" in the middle of the harbor to the Wellfleet town landing; and a 10-foot-deep anchorage area, 500 feet long and 800 feet wide, adjacent to the town wharf.