The station’s airfield is operated and maintained by Naval Station Mayport’s Air Operations Department. The airfield can accommodate any DoD aircraft and conducts more than 100,000 helicopter and fixed-wing flights each year. Military passenger flights are available through the air terminal, which processes about 13,000 passengers each year. The department also provides air traffic control services, air terminal and servicing functions for transient aircraft, field arresting gear, and ground electronics maintenance.

Naval Station Mayport Port Operations is comprised of  the Waterfront Services, Surface Coordination, Service Craft, and Administration Support divisions.

Located in Building 2078, the Port Operations Department, with more than 100 military members and civilian employees, is also responsible for ships' berthing requirements. Port Operations also provides pilot, tug, spill response, tow assistance, emergency personnel transfers at sea, and degaussing range services.