Natural resource management at the park has three major objectives: protect and promote biological diversity and habitat health; protect and promote soil and water quality; and protect and enhance the cultural landscape. To meet these objectives, inventory and monitoring programs are conducted on water quality; bird, mammal, reptile, amphibian, and fish populations; vegetation communities; and forest health. Research is also conducted to understand past land uses and their impacts on the natural resources and the landscape today. Finally, all of this information is used to develop goals and strategies that guide natural resource management.

Active resource management at Appomattox Court House National Historical Park addresses many issues that are directly related to the poor land management practices of the past 250 years. Loss of soil fertility due to erosion, introduction of non-native invasive plants and animals, loss of wetlands, loss of mature forests, and loss of native plant and animal species are legacies of the past. Efforts to improve wildlife and plant communities and historic landscapes must deal with these issues. Additionally, the park faces possible threats through nearby land development, the introduction of new plant and wildlife diseases and pests, and climate change.