"An Act Providing for the Formation, Government and Operation of Harbor Districts, the Calling and Conducting of Elections in such District of Harbor Commissioners, defining their powers and duties, and providing for the issuance and disposal of bonds of such Harbor District, and providing for the assessment, levy and collection of taxes for the payment of such bond and for the ordinary annual expenses of such Harbor District," was approved on June 10, 1931, and is found in the Statutes of 1931 at page 1483.

Under the authority of this Act, the San Mateo County Harbor District was established, in 1933, by a Resolution of the Board of Supervisors, who established the entire area of the County of San Mateo as the District's boundaries.

The District was originally formed to build a harbor at Redwood City, but the Great Depression intervened.

Coastsiders then pushed to get a breakwater built at Pillar Point for a harbor of refuge for the fishing fleet. The Army Corps of Engineers began work on this breakwater after World War II and finally completed it in 1961. The Johnson Pier, docks and 369 berths, and the inner breakwater were built during the 1970's and 1980's. Pillar Point remains a major commercial and sport fishing harbor, with 369 berths, on California's central coast, and is host to many public events including the annual Mavericks surfing competition, the July 4th fireworks display, and the Christmas boat decorating contest.

The District took over operation of Oyster Point Marina/Park from the City of South San Francisco in 1977. It then completed construction of docks and 589 berths, a new breakwater, and onshore facilities during the 1980's. The District diversified this recreational marina bringing in ferryboat service (134 of 589 berths were removed to accommodate ferry service, resulting in 455 berths) to the East Bay, dining cruises, marine educational programs, and cooperation with the City on area redevelopment.

The District is governed by a five member Board of Harbor Commissioners, who are elected County-wide for staggered four-year terms.