Hardwood stands in the Reserve consist primarily of oaks, maples, and hickory. 

Conifers in the reserve are dominantly pine and hemlock. Minor populations of cedar and tamarack also exist. In 1970, the Wisconsin Department of Natural Resources planted white pine plantations throughout the Reserve. As part of the Reserve Master Plan, these will be harvested over time and replanted with red and white oaks.

Agriculture: The Kickapoo Valley Reserve leases over 700 acres to area farmers for agriculture production. Crops typically include corn, soy beans, or alfalfa. Users of the Reserve are welcome to hike and hunt through these fields, observing all respect for the crops. 

Wetlands consist of approximately 17% of the Reserve. These areas are important to absorb rain/snow runoff, retention of soil, provide wildlife habitat, and can serve as filters for pollutants. Since the displacement of the farms, many agriculture fields returned to wetlands. As a result of the 2003 Highway 131 Project, the Wisconsin Department of Transportation mitigated 30 acres for wetlands. 

Open Areas: Many open areas of the Reserve are former agricultural fields. The Land Management Plan intends to maintain these as open areas. Native grass restoration efforts include over 75 acres. The Ho-Chunk Nation, the Prairie Enthusiasts (Coulee Region Chapter), Department of Natural Resources Turkey Stamp Fund, and Wisconsin Department of Transportation have assisted in these restoration efforts.

For comparison of the changes of land cover see the 1840 Finley Map(pdf), the 1930 Bordner Survey Map(pdf) and the 1990's Land Cover Map(pdf).