Before Bard's 900-foot wharf opened in 1872, goods destined for offshore vessels had to be ferried through the surf zone — a difficult and dangerous operation. The submarine canyon off Point Hueneme eliminated that problem, and the port quickly became a hub for grain, lumber, lima beans, and sheep. Three- and four-masted wooden schooners made the run between here and San Francisco with regularity. By 1897, the wharf had been extended to 1,500 feet. It was a remarkable rise — and a short one. When the railroad reached the region and the coast route between Los Angeles and San Francisco was completed in 1904, maritime traffic collapsed almost overnight.

The modern port was born of necessity in the 1930s and forged by war in the 1940s. The Harbor District formed on April 29, 1937. When World War II began, the Navy saw what Bard had seen decades earlier: deep water close to shore, relatively sheltered from open ocean swells. The Advance Base Depot began operating here on May 18, 1942, supplying the Naval Construction Force — the Seabees — whose equipment and materiel moved through the port en route to the Pacific Theater. The base became Naval Construction Battalion Center in 1945, and today operates as part of Naval Base Ventura County. The military never left. The Navy controls all ship movements in and out of the harbor, making this one of the few genuinely shared civilian-military ports on the West Coast.

The modern Port of Hueneme is a specialist port, deliberately so. It handles cargo that the giant container ports in Los Angeles and Long Beach are not designed for: automobiles, fresh produce, and roll-on/roll-off freight. Automotive cargo accounts for 85 percent of the port's total cargo value. Vehicles from South Korea, Germany, and Japan arrive here and fan out to dealers across a dozen western states. Bananas were the port's highest-volume product in 2014, with Chiquita making it the second-largest banana port in the nation. During the 2021 global supply chain crisis, when container ships queued for weeks outside Los Angeles, shippers looked north to Hueneme as a pressure valve. In 2019, the annual cargo volume was 1.6 million tons — worth an estimated $9 billion.

The port has developed a few traditions that don't appear in shipping manifests. About 250 feral cats live on port property, managed by a volunteer group that feeds them three times a week and runs a trap-neuter-return program to keep the population stable — and the rat population in check. The port also handled the dive boat MV Conception after it caught fire and sank near Santa Cruz Island in September 2019, killing 34 people, providing a secure location for federal investigators. And when the COVID-19 pandemic hit, the port partnered with World Central Kitchen and local restaurants to channel fresh produce directly to farmworkers and packinghouse employees who couldn't reach food banks during working hours.