The Port of Anacortes is a US port-of-entry and a popular destination for boaters. The Port of Anacortes owns and operates the Cap Sante Marina, offering both permanent and transient moorage including up to 200 berths for guest moorage. Floats equipped with electric power and water can accommodate vessels to 36.6 meters (120 feet) in length.

The well-maintained slips and docks in the Port of Anacortes's Cap Sante Marina are open seven days a week from 8am until 5pm. They offer large restrooms with showers, lighted walkways, and convenient loading and parking areas. The Cap Sante Marina is within easy walking distance to shops, restaurants, grocery, and marine stores in the Port of Anacortes.

Located near Cap Sante Head off Fidalgo Bay, the Port of Anacortes' marina has 950 slips, including space for up to 200 guest boats. The marina has a fuel dock with gas and diesel, a pump-out station, a trailer boat launch sling, and a small craft hoist with lifting capacity for up to 3600 pounds. The trailer boat launch in the Port of Anacortes' Cap Sante Marina operates from 8am until 6pm in the summer and 5pm in fall and winter. With a well-trained full-time staff, the launch has a new high-speed monorail hoist with capacity for boats to 11.3 meters (37 feet) in length up to 12 tons.

The Port of Anacortes' Cap Sante Boat Haven, the commercial port area, contains three berthing areas. Float A is used to moor fishing and commercial vessels. The South Harbor Park and a parking lot are located at the rear of the float which has berthing distance of 137.2 meters (450 feet) with alongside depths of 2.4 and 3.0 meters (eight and ten feet).

The T-Dock in the Port of Anacortes' Cap Sante Boat Haven is used to receive seafood and handle supplies, equipment, and nets for fishing vessels. A work space for fishermen and parking is located at the rear of the Port of Anacortes' T-Dock which has berthing distance of 57.9 meters (190 feet) with alongside depths of 2.4 and 3.0 meters (eight and ten feet). With a depth of three meters (ten feet), the Cap Sante Boat Haven in the Port of Anacortes also has Float B used for mooring fishing vessels.

Dakota Creek Industries is a Port of Anacortes tenant operating a ship-building and repair facility between Piers 1 and 2. Port of Anacortes offices are located at Pier 1 which also supports Dakota Creek Industries. Pier I is owned by the Port of Anacortes and operated jointly by the Port of Anacortes and Dakota Creek Industries. Pier I is used to ship and receive conventional general and heavy-lift cargoes, moor vessels, and moor Dakota Creek Industries' 9000-ton floating dry dock.

At the rear of the Port of Anacortes' Pier I are transit sheds and six storage warehouses, one of which is used for public storage. Pier 1 has berthing distance of 173.7 meters (570 feet) with alongside depth of 10.1 meters (33 feet), and plans are underway to dredge the pier to a depth of 13.4 meters (44 feet). The Port of Anacortes' Pier 1 covers an area of 1.5 acres and can support live loads to one thousand pounds (453 kilograms) per square foot. With truck access to the warehouses, Pier 1 also has immediate access to downtown Port of Anacortes.

Curtis Wharf in the Port of Anacortes is a working wharf and dock for commercial vessels that include vessels of the US Navy and tenants staging and assembling project cargo vessels. The Port of Anacortes' Curtis Wharf has berthing distance of 104.9 meters (320 feet) and includes dolphins of 146.3 meters (480 feet) with alongside depth of 8.5 meters (26 feet) with plans to dredge to a depth of 11.6 meters (38 feet). Covering an acre, the Curtis Wharf in the Port of Anacortes can handle live loads to 1200 pounds (544 kilograms) per square foot.

Used for exporting dry bulk cargoes and for short-term mooring of barges and other vessels, Pier II in the Port of Anacortes is operated jointly by the Port of Anacortes and Anacortes Log & Bulk Stevedoring. Cargoes include petroleum coke and logs. Covering 5.45 hectares, Pier II has berthing distance of 140.8 meters (462 feet) and includes dolphins of 345.3 meters (1133 feet) with alongside depth of 11.1 meters (36.5 feet). The Port of Anacortes' Pier II can handle live loads of 750 pounds per square foot (3700 kilograms per square meter). Pier II in the Port of Anacortes has a 13.5-acre open storage area that can accommodate five million board feet of logs. It also has a truck wash facility and a stationary ship loader.

The Anacortes Ferry Terminal serves passenger ferries between the Port of Anacortes and the San Juan Islands. Located half way between Vancouver and Seattle, it is the only link between the San Juan Islands and the mainland. The Port of Anacortes Ferry Terminal contains a waiting room and food services that include the Cheesecake Café and vending machines for snacks. Except during winter sailing schedules, vessel galleys offer food service aboard the ferries. Passengers can board bicycles, motorcycles, and vehicles, although space can be limited. Scheduled ferries travel to Lopez, Shaw, and Orcas Islands and to Friday Harbor on San Juan Island.

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