Moss Landing Harbor lies on the eastern shores of Monterey Bay in south central California about 25 kilometers northeast of Monterey Bay Harbor and some 154 nautical miles south-southeast of the Port of San Francisco. Located at the mouth of Elkhorn Slough, Moss Landing Harbor is the base of the California State University's multi-campus research facility, the Moss Landing Marine Laboratories. When it was founded in 1895, it was named Moss Landing after Charles Moss who built a wharf at the site. During the early years, Moss Landing Harbor was a busy whaling port. In 2005, some 782 people lived there.

When California was admitted to the United States, the area that makes up today's Moss Landing Harbor was received in trust from the federal government by the State. The lands, tidelands, and submerged lands along the Salinas River were planned for commercial, fishery, and navigation purposes.

Retired ship captain Charles Moss brought his family from Texas to build a homestead in California in 1866. Partnering with Portuguese whaler Cato Vierra, Moss built a 61-meter wharf at the site of the future Moss Landing Harbor to create a commercial pier. The wharf invited whalers, fishermen, and salt pond operators to Moss Landing Harbor. The port was soon busy, traffic boosted by gold rush fever when Moss Landing Harbor exported goods like potatoes, lumber, and sugar beets to booming San Francisco. Moss sold his holdings in Moss Landing Harbor to the Pacific Coast Steamship Company, but the town respected him enough to adopt his name. Unfortunately, the wharf and much of the town's infrastructure were destroyed by an earthquake in 1906.

The railroad arrived in 1890 when the Pajaro Valley Consolidated Railroad was built to connect Spreckels to Watsonville, passing through Moss Landing Harbor. Presence of the railroad further increased seaborne traffic. A large whaling station was founded in Moss Landing Harbor in 1917 which was replaced in 1931 by a fish canning plant. More fish processing plants began to appear in the area as well. Recognizing the port's ideal location in the center of Monterey Bay, community leaders began a plan for an inland harbor at Moss Landing.

In 1943, the Moss Landing Harbor District was created to develop a harbor there. The Harbor District Board executed an easement and franchise agreement with landowners, gaining a right-of-way over about 13 acres of land. A harbor channel would be constructed through the new Moss Landing Harbor land.

In 1945, the US Army Corps of Engineers began construction of the Moss Landing Harbor. By 1947, the dredging was finished, and wharves and piers were completed. The new port was officially opened that year. Unfortunately, the fishing industry faced rapid decline in the mid-20th Century as the whale population decreased, whale product prices fell, and offshore factory ships introduced new competition. At the same time, the sardine industry was disappearing due to overfishing, and many local warehouses and canneries went out of business. The Moss Landing Harbor District was forced to seek other income sources.

Fishing revived eventually, and the city's debts were slowly repaid. After that, the Moss Landing Harbor District began to develop the harbor once again. One of the franchise agreements they entered into was the Pacific Gas and Electric power plant, constructed in 1950, which became the second biggest fossil fuel thermal electric power plant in the world and is today the city's most visible landmark.

The Elkhorn Yacht Club added 60 mooring spaces and club facilities in Moss Landing Harbor in 1951. In 1952, shipments began to arrive from Texas when gasoline storage facilities were completed.

In 1967, the Moss Landing Harbor land grant was increased by the Governor of the State of California. This added tidelands, submerged lands along the Salinas River, and about six hundred meters seaward to the Moss Landing Harbor District. The land was added so that the Harbor District could build, maintain, and operate additional wharves, docks, piers, and slips to promote commerce and navigation.

The economy of the modern Moss Landing Harbor centers on its role as a fishing port and tourist destination. Other important contributors to the economy include the international research institutes, nature and whale-watching tours, sports fishing charters, industrial trades, and industrial trades.

In 2007, a $4 million North Harbor Improvement Project was completed that added to Moss Landing Harbor a new four-lane boat launch ramp, new parking, storm drains, a boat wash, and a 274-meter public access wharf with an alongside 33-meter visitor serving dock. The county transportation agency also added a pedestrian and bicycle trail to run along the perimeter of the North Moss Landing Harbor. Furthermore, private interests are constructing a restaurant overlooking the harbor.

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