The City of Monterey is the port authority for the Monterey Harbor and Marina. In addition to travelers and tourists, Monterey Harbor attracts thousands of fishers and boaters each year. The Harbormaster, under the supervision of the City Council, is responsible for regulating traffic and use of Monterey Harbor and to promote better access to the waterfront area.

Monterey Harbor Municipal Marina is open 24 hours a day. Boats must get their berthing or mooring assignment from the Harbor Office to dock there. Visiting boats are accommodated as they arrive, and there are no reservations. Today, the Monterey Harbor Municipal Marina offers 413 slips ranging from 6.1 to 15.2 meters in length. The Marina offers six end ties for boats from 12.2 to 22.9 meters long. The marina also serves long-term tenants through slip license agreements with the City. Slip licenses are transferrable with sale of boats. A waiting list is maintained by the Monterey Harbormaster. Adjacent to the Harbormaster's Office are two launch ramps available for use with no ramp fees.

The Monterey Harbormaster also manages the outer harbor, a designated special anchorage area with about 150 privately-owned mooring buoys. A city license is required for mooring. The outer harbor can accommodate about 20 live-aboard boats.

The City of Monterey operates a seasonal East Mooring Program by permit from the state and the Monterey Bay National Marine Sanctuary where boats of 15.2 meters and less can anchor in Monterey Harbor from April through October. Monthly rental includes a dinghy space, and boaters that participate in the program in the summer have the opportunity for a slip in the Marina during the winter. An open anchorage area east of Wharf II and the East Moorings is also available where boats can anchor for no more than 30 days in a 6-month period.

Monterey Harbor's Municipal Wharf II is the easternmost structure in the harbor. Installations at Wharf II include five wholesale fish companies, a commercial abalone farm, and the Monterey Peninsula Yacht Club as well as restaurants, a snack bar, and public restrooms. The Yacht Club offers limited reciprocal berthing at its private dock. Commercial dive charters operate from Monterey Harbor's the "Yellow Boat Dock" on the west side of Wharf II outside the Marina's seawall. Extending from Wharf II is a 213.4-meter fishing promenade where anglers can fish from the east side of the wharf without a fishing license, although sport fishing is not permitted near the commercial facilities. Wharf II also offers a 3-ton token-operated public boat hoist that is available 24 hours a day.

In the early 1930s, the US Army Corps of Engineers constructed a 518-meter breakwater to protect the north side of Monterey Harbor. After that, a wharf was built on the breakwater as home port for the US Coast Guard Cutter Long Island. Today, the Coast Guard berths small boats at the Coast Guard Wharf, offering 24-hour emergency services. During daylight hours, the wharf is open to the public, and fishing is permitted on the north side of the breakwater.

Monterey Harbor hosts some cruise ships. They maintain a schedule of cruise visits on their website.

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