The City of Juneau Docks and Harbors Board operates and manages the port and waterfront facilities in the Port of Juneau. The nine-member citizen board oversees the city's Docks and Harbors Department. Appointed by the Board, the Port Director is its chief executive, and the staff includes the harbormaster, a port engineer, an administrative officer, and a secretary. Financed through user fees, leases, fisheries business taxes, and federal and state grants, the Port of Juneau Docks and Harbors Department operates without subsidies from local taxes. Special local sales taxes fund specific port projects.

Port of Juneau facilities include two commercial loading facilities, two cruise ship docks, several small boat floats and harbors, launch ramps, two boat yards, and a large area of tidelands and waterfront properties. All of the public slips in the Port of Juneau are assigned by the harbormaster.

Public facilities in the Port of Juneau include the intermediate vessel float that provides almost 244 meters of moorage in the downtown area. Used for short-term stays, this moorage area is very busy, and boaters should arrange in advance for a spot. Also near downtown, the Port of Juneau's Harris Harbor offers limited moorage on a first-come, first-served basis when permanent tenants are out. Aurora Basin is located adjacent to Harris Harbor in the Port of Juneau, but no transient moorage is allowed in the basin.

The Auke Bay Harbor is located almost 20 kilometers north of the Port of Juneau and is connected by road to the city. Boats are sent here when downtown space is limited. The Don D. Statter Harbor facilities in Auke Bay Harbor offer 1.8 kilometers of transient moorage for vessels up to 61 meters long. Moorage for short-term stays is assigned on a first-come, first-served basis by the Port of Juneau harbormaster. Amenities are available like showers, water, and pump-out services. The Amalga Harbor is located about 38 kilometers north of the Port of Juneau, and it contains a boat launch.

The Port of Juneau also has several private marinas that do not offer transient moorage but do offer many services for boaters. Just south of downtown Port of Juneau, UNOCAL Dock offers gas, diesel, and lubricating oils. The Tesoro Dock next to downtown Port of Juneau's Aurora Harbor is a fuel dock offering gas and diesel.

Directly across the Port of Juneau channel from the Harris Harbor is the Petro Marine Fuel Dock offering diesel, unleaded gas, and Chevron lubricants. Fisherman's Bend in Auke Bay offers gas, diesel, and boat repairs. Also in Auke Bay, the DeHarts Marina in the Port of Juneau offers commercial and non-commercial fueling facilities operated by Union Oil Diesel. It also offers regular gasoline and engine oils. The DeHarts boat yard has a 15-ton travelift and offers bottom pointing, cleaning, and minor boat repairs.

The Port of Juneau's Seadrome Marina is located downtown and provides 170.7 meters of moorage. It also offers potable water, electricity, fuel, and shore-side services. Boaters should make reservations before arriving at the Seadrome Marina. Donohue's Marina is located almost 30 kilometers north of the Port of Juneau. Called "Tee Harbor" by locals, Donohue's Marina is a public anchoring harbor and offers gas and diesel at the dock.

The Auke Bay Loading Facility in the Port of Juneau was opened in 2009. Due to the increased development of the islands, bays, and harbors near the Port of Juneau over the last 25 years and the stiff competition for moorage space by personal and recreational vessels, local water transport businesses asked for a separate facility devoted to handling heavy equipment and building supplies. The Port of Juneau's Auke Bay Loading Facility met that demand.

The Port of Juneau is currently improving several port facilities to better meet the needs of its users. Douglas Harbor is being renovated. Statter Harbor in Auke Bay is being improved and expanded to include additional moorage and improved facilities for harbor users. Improvements are also planned for the downtown cruise ship facilities.

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