Cowpen Lake is located in western Putnam County, Florida. The lake is located within the Interlachen Sand Hills of the Central Lakes District. The area around the lake is dominated by many small lakes and marshland, particularly Levys Prairie to the north. The lakes and prairies in this region occupy dissolution valleys, where sinkholes coalesce to form small, irregular-shaped lakes. Cowpen’s shoreline is very irregular, with a perimeter of 11.5 km and a surface area of 2.8 km². Lake level in March of 1995 was 26 m (85 ft) NGVD.