San Joaquin Harbor lies on the southern shores of the San Joaquin River about six nautical miles upriver from Pittsburg, California. It is also about 38 kilometers (24 miles) west-northwest of Stockton. San Joaquin Harbor is about half-way between Antioch and Oakley, although it is in a relatively unpopulated area.

San Joaquin Harbor is home to the Fulton Shipyard Pier where vessels moor for repairs, conversions, and outfitting. The pier has two surface rail tracks that connect with the Burlington Northern Santa Fe Railway, and a marine repair plant is located at the rear of the pier. This San Joaquin Harbor pier has berthing space of 160 meters (525 feet) with alongside depth of five meters (16 feet) MLLW.

Georgia-Pacific Corporation owns and operates the Antioch Plant Wharf in San Joaquin Harbor to receive gypsum rock carried in by self-unloading vessels. One surface rail track at the wharf connects to the Burlington Northern Santa Fe Railway. This San Joaquin Harbor wharf has a steel-frame storage dome with capacity for 38 thousand tons of gypsum rock, and a plant that manufactures gypsum board is located at the rear of the Antioch Plant Wharf. The wharf has berthing distance of almost 238 meters (780 feet) with alongside depth of 9.4 meters (31 feet) MLLW.

The California Mill Wharf in San Joaquin Harbor is owned by Gaylord Container Corporation and operated by Richmond Stevedoring Company, Inc. The wharf is used to receive various dry bulk commodities. Rail tracks linking to the Burlington Northern Santa Fe Railway serve the wharf. One 16-inch pipeline connects this San Joaquin Harbor wharf to a 72 thousand barrel fuel oil storage tank. A paper mill is located at the rear of the wharf. The California Mill Wharf has berthing distance of 233 meters (766 feet) with alongside depth of 10.7 meters (35 feet) MLLW.

Gaylord Container Corporation owns the California Mill Pier at San Joaquin Harbor. The pier has one surface rail track that connects to the Burlington Northern Santa Fe Railway. A ten-inch pipeline connects the wharf to two steel fuel oil storage tanks with total capacity for 200 thousand barrels. A six-inch pipeline connects the wharf to a 24 thousand gallon caustic soda storage tank at the rear of the wharf. This San Joaquin Harbor pier has berthing distance of 30.5 meters (100 feet) with alongside depth of 6.1 meters (20 feet) MLLW.

The Pacific Gas and Electric Company owns the San Joaquin Harbor Contra Costa Power Plant Wharf. The wharf is served by one surface rail track connecting to the Burlington Northern Santa Fe Railway. At one time, the wharf was used to receive fuel oil for consumption at the power plant. A 12-inch pipeline connects the wharf to eight insulated storage tanks with total capacity for 2.1 million barrels. The storage tanks are connected to the Delta Power Plant by inland pipeline. This San Joaquin Harbor wharf has berthing distance of 45.7 meters (150 feet) with alongside depth of 4.9 meters (16 feet) MLLW.

The San Joaquin Yacht Harbor Marina, located half-way between San Francisco and Sacramento, is located on the south side of the Sacramento River adjacent to the Antioch bridge. This San Joaquin Harbor marina is a private club with transient slips served by water and power hook-ups. Amenities at the San Joaquin Harbor marina include showers, restrooms, and a grocery store. The park-like marina grounds are equipped with a horse shoe pit and a picnic and barbecue area. Temperatures range from an average high of 23°C (73.5°F) in August to an average low of 5°C (41°F) in January.

The Antioch/Oakley Regional Shoreline, located north of the intersection of Bridgehead Road and Wilbur Avenue in San Joaquin Harbor, has a 167.6-meter (550-foot) pier for fishing in the San Joaquin River.

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