The Harbors Division within the State of Hawaii's Department of Transportation manages the Port of Kailua Kona. The Harbors Division plans, designs, builds, operates, and maintains State water transportation facilities. They also coordinate with other government agencies and programs to assure the efficient and effective operation of Hawaii's commercial harbors. At present, the Harbors Division manages ten commercial harbors, including the Port of Kailua Kona.

Many scuba dive and fishing charter boats that operate off the west side of Hawaii island use the Port of Kailua Kona's Honokohau Marina and Small boat Harbor. Just 6.4 kilometers (4 miles) from the Kona Airport, the popular sport fishing vessels Kona Spirit and Hustler make this Port of Kailua Kona small boat harbor their home. The Charter Desk in the Port of Kailua Kona conducts fish weigh-ins two times each day.

The State of Hawaii's Department of Land and Natural Resources owns and operates the State of Hawaii Kona Pier in the Port of Kailua Kona for mooring of fishing and excursion vessels and boarding passengers. This Port of Kailua Kona Pier has berthing space of 24.4 meters (80 feet) with alongside depth of 5.2 meters (17 feet) MLLW.

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