The board establishes policies under which the port's staff – supervised by the Executive Director – conducts its daily operation.

In 1980, the port completed a wildlife refuge in Chula Vista in an effort to improve the ecological balance of the Bay.

In 1990, The Pasha Group began importing vehicles (Isuzus) at the National City Marine Terminal.

The National City Marine Terminal is a 125 acres (0.51 km2) seven berth facility operated by The Pasha Group, which processed over 450,000 vehicles during fiscal year 2016.

The National City Marine Terminal serves as the primary port of entry for Honda, Acura, Isuzu, Volkswagen, Nissan, Mitsubishi Fuso, and Hino Motors.

The main facility, at B Street Pier in downtown San Diego, along North Harbor Drive, has three cruise berths.

[9] By 2011, the number of ship calls had fallen to 103, a decline blamed on the slumping economy as well as fear of travel to Mexico due to well-publicized violence there.

[10] On July 13, 2016, Vice President Joe Biden made a visit to the port, delivering a speech at the Tenth Avenue Marine Terminal.

[12] Ships sometimes make unscheduled stops in San Diego because of storm warnings along the Mexico cruise route.

[13] In July 2022, the port held a groundbreaking ceremony for a $1.35 billion project to construct a resort hotel and convention center on the Chula Vista Bayfront.

[15] The Port of San Diego has assisted in the restoration and enhancement of over 280 acres (110 ha) of environmental habitat including Emory Cove, and the Chula Vista Wildlife Reserve.

Revenue from real estate assets and developments, primarily building and ground rents and concession fees, was approximately $96 million in FY 2014–2015.

The Port of San Diego collects rents from many hotels, restaurants, parking facilities, yacht clubs, etc.

NASSCO is the largest new-construction shipyard on the west coast of the United States; "specializing in auxiliary and support ships for the U.S. Navy and oil tankers and dry cargo carriers for commercial markets.