Morro Bay Harbor is located in San Luis Obispo County, California, in the United States. It is some 166 kilometers southeast of Monterey Harbor and over 300 kilometers northwest of the Port of Los Angeles. This natural bay has an artificial harbor built by the US Army Corps of Engineers during World War II. Morro Bay Harbor is the only all-weather harbor for small commercial and recreational boats between Monterey and Santa Barbara. Morro Bay Harbor's major landmark, Morro Rock, was surrounded by water before the Corps of Engineers built a breakwater and road across the harbor. In 2000, over ten thousand people lived in Morro Bay Harbor.

Before Europeans arrived in Morro Bay Harbor, the Chumash people inhabited the area around Morro Creek's mouth. A large settlement existed along the Morro Creek's banks and terraces.

In 1542, Juan Rodriguez Cabrillo from Portugal discovered and named Morro Rock as he explored the Pacific Coast for Spain. Morro Rock looked much like the turbans worn by the Moors. In 1587, immigrants from the Philippines arrived in Morro Bay Harbor aboard a Spanish galleon.

While Mexico controlled the area, cattle and dairy ranches were formed in the Morro Bay Harbor area by Spanish land grants. The port at Morro Bay Harbor grew to bring imported goods to the ranchers and to export their crops and animals.

Franklin Riley founded the town of Morro Bay in 1870, formalizing the role of Morro Bay Harbor for exporting ranch and dairy products. The wharf he built became today's Embarcadero. Schooners arrived regularly at Morro Bay Harbor to load potatoes, wool, dairy, and barley.

During the mid-20th Century, Morro Bay Harbor was home to an abalone fishing industry that peaked in 1957 before overfishing began to decrease the catch. Yet, Morro Bay Harbor is still a busy fishing port where both commercial and sport fishers bring in sole, halibut, rockfish, and albacore. Sport fishing is now an important part of the local economy. There are also oyster farms in the shallow areas of the back bay. Modern Morro Bay Harbor relies primarily on its beautiful beaches and tourism.

Some parts of Morro Bay Harbor are a national and state bird sanctuary, an estuary, and a state wildlife refuge. California recently declared Morro Bay Harbor as a California Marine Reserve.

Morro Rock, the Morro Bay Harbor's outstanding natural landmark, is a volcanic plug at the entrance to the harbor. From the late 19th Century until 1969, Morro Rock was quarried. Since that time, it has been a reserve for the endangered peregrine falcon, so visitors cannot go on the rock itself. They can visit the base of Morro Rock. Climbers who dare to venture on the prohibited rock can expect fines or jail visits, and they can also risk life and limb on the loose rocks that frequently fall.

South of Morro Bay State Park Marina, the Morro Bay Harbor back bay is shallow with some channels that are unmarked and hard to navigate. They are also full of eel grass on which boats can snag or propellers can clog. Boats also run aground easily in this area, especially at low tide.

A US Navy base that trained sailors to operate landing craft was located on the north side of Morro Bay Harbor during World War II.

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