Water in the Boundary Canal generally flows south and east along the western boundary and south along the eastern boundary, converging at the stormwater reservoir located on the eastern side of the base. Water flows through water-control structures out of the stormwater reservoir into the Outfall Canal. The land between Homestead AFB and Biscayne Bay is composed of farmland, nurseries, woodlands, and forested wetlands. Homestead AFB and these lands are part of the drainage basin for the canal. Biscayne Bay is part of the Biscayne National Park.
Mystic Lake is located near a former recreational campground and trailer area.
Phantom Lake is located near a controlled area where access is limited. Land use adjacent to the northern and western borders of the base includes residential and commercial facilities within the city limits of Homestead. Homestead AFB is surrounded by a fence. The Biscayne Aquifer is the primary source of drinking water in southern Florida. It consists of highly permeable limestone, sandstone, and sand.