Headquarters Pond is named for its proximity to the second refuge headquarters. Along with Picnic Pond, it was once tidal but both are now managed as brackish pools. An accessible trail leads from the restroom parking lot to an observation deck.
In close proximity are Picnic Pond, Tower Pond, the Restrooms and a fire tower. On the opposite side of the parking lot from the observation deck trail is a one-mile interpretive trail which goes by the base of the fire tower and around Tower Pond.
Purple Gallinules breed in summer. Wading birds and alligators can be seen all year, and Night-Herons roost here. The fire tower, no longer used as a lookout, is a favored haunt of Black Vultures and Turkey Vultures.