The Port of Key West is a City department responsible for maritime and real estate services and infrastructure management to support the local economy, provide recreation, and protect the social and marine environment.

Recently, the City has changed its approach to Port of Key West waterfront management. City waterfront responsibilities, including the deep-water port, have been consolidated into the Port Operations department. The department coordinates cruise ships and Navy vessels, develops port-related properties, and acts as liaison to the Key West Bight Board and the Port Advisory Board.

Recognizing the vital importance of the waterfront, the Port of Key West hopes to improve waterfront operations by making them more effective and efficient, improving accountability in port management, and improving consistency in the implementation of Port of Key West policies and procedures.

In 1969, the first cruise ship, the Sunward, arrived at the Navy's Truman Annex Pier (also called the Navy Mole) in the Port of Key West. In 1984, the Port of Key West opened a pier on Mallory Square over some opposition. Today, cruise ships dock at all three Port of Key West piers. In 2009, almost 860 thousand cruise passengers arrived at the Port of Key West.

The Key West Bight is located in the Port of Key West's historic district. It blends historic and modern Key West in a charming is a 20-acre waterfront facility. From Key West Bight, visitors can go diving, parasailing, or fishing. They can take a trip on a historic schooner. The Port of Key West's HarborWalk at Key West Bight is bordered with food-oriented businesses and fine restaurants. The Marina at the Port of Key West Bight contains 33 deep-water transient ships that can accommodate vessels up to 42.7 meters (140 feet) long with 3.7-meter (12-foot) draft throughout the year. The slips are served by on-site showers, laundry, and pump-out facilities.

The Port of Key West owns and operates the City Marina at Garrison Bight on the Port of Key West's north side. The Marina contains 250 slips at the Palm Avenue Causeway. It has been home to the Charter Boat Row since the 1930s. There is also a community of live-aboard homes in the Marina. In addition, the Port of Key West City Marina has 30 transient slips on concrete floating docks with amenities that include 24-hour security, showers, vessel pump-out services, an on-site coin-operated laundry, 30- and 50-amp power, trailer storage, and trash removal storage. There is no dry boat storage at the Port of Key West City Marina. The Port of Key West City Marina can accommodate vessels to 21.3 meters (70 feet) long.

Key West Express provides service to the Port of Key West from Fort Myers Beach year-round and from Marco Island seasonally. The Key West Bight Ferry Terminal is located in the Key West Bight Historic Waterfront. The modern air-conditioned ferries have sundecks, big-screen TVs, cocktails, and a snack bar. Depending on weather conditions, travel time between Fort Myers and the Port of Key West is about 3.5 hours. Since 2007, ferry service between Miami and the Port of Key West has run Friday through Sunday.

The underwater Key West Marine Park was created to better protect the near-shore coral reef ecosystem while also providing compatible uses for beach visitors, swimmers, and boaters. Separate lanes are provided for swimmers and boaters. The Port of Key West Marine Park is a voluntary no-harvest zone so that fish habitat is protected. The White Street Pier in not contained within the park so that people can fish on the pier.

North of the Port of Key West City Marina, between Sigsbee Park and Fleming Key, is the Garrison Bight Mooring Field. The 149 moorings host a mix of full-time live-aboard and transient borders. Each mooring system is inspected every three months.

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