The ferry terminal of the Alaska Marine Highway system is also located further out the road in Auke Bay at about 14 miles.

The Coast Guard cutter Liberty was homeported at the Auke Bay Harbor for 33 years, before being reassigned to Valdez, Alaska in 2022.

The United States Coast Guard Cutter Reef Shark, a Marine-Protector Class Patrol Boat, is homeported out of Auke Bay / Statter Harbor.

The cutter's primary mission set includes law enforcement, search and rescue, military operations, and environmental protection.

During the summer months, USCG Small Boat Station Juneau maintains a 45' Motor Lifeboat at Reef Shark's moorings, providing a faster search and rescue asset as well as law enforcement capability to the immediate harbor area.

In 1940 it was renamed Alaska Clipper and flew from Matthews Beach on Lake Washington in Seattle to Auke Bay stopping in Ketchikan.

[19] The 4-acre facility was declared surplus by the US Government in 2016, after the Auke Bay Laboratories’ headquarters was moved to the new Ted Stevens Marine Research Institute in 2007.