Innan bildandet år 2000 hade dessförinnan USA:s atlantflotta bidragit med sjöstridskrafter till USSOUTHCOM. Från början var högkvarteret för USNAVSO beläget vid Naval Station Roosevelt Roads på Puerto Rico men flyttade under 2004 till Naval Station Mayport utanför Jacksonville i nordöstra Florida.
^”SOUTHCOM Component Commands & Units” (på engelska). www.southcom.mil. United States Southern Command. https://www.southcom.mil/About/SOUTHCOM-Components-and-Units/. Läst 6 november 2021. ”Located at Mayport Naval Station, Jacksonville, Florida, U.S. Naval Forces Southern Command/U.S. Fourth Fleet (USNAVSO/FOURTHFLT) employs maritime forces in cooperative maritime security operations in order to maintain access, enhance interoperability, and build enduring partnerships that foster regional security in the U.S. Southern Command Area of Responsibility (USSOUTHCOM AOR).
USNAVSO/FOURTHFLT Lines of Operation:
1. Security Cooperation Activities
2. Maritime Security Operations
3. Contingency Operations”