Lake Wauberg is located south of Paynes Prairie in central Alachua County. The lake is in the Ocala Uplift District, situated between the forested highlands of the Fairfield Hills area and the surrounding dissolution valleys of the Alachua Prairies. Lake Wauberg is irregular in shape, covering 1.6 km² with about 5 km of shoreline. The lake is adjoined to the east by Sawgrass Pond. A marshy area to the northwest is separated from the lake by a topographic high.