Harmonie State Park contains two nature preserves operated by the Indiana Department of Natural Resources (IDNR).
The Wabash Border preserve contains a mature dry-mesic upland forest, mesic ravine forest, and wet floodplain forest bordering the Wabash River.
The Harmonie Hills nature preserve contains one of the largest tracts of mature mesic upland forest in the Southwest Lowlands Natural Region. Several rare fish species are found in Road Brook.
These community types along with their expected component flora and fauna contain species that are area-sensitive forest interior plants and animals dependent upon large, un-fragmented forest ecosystems.