The National Wildlife Refuge System Improvement Act of 1997 (NWRSIA) and the “Biological Integrity, Diversity and Environmental Health Policy” formalized the concept of biological integrity as a federal wildlife refuge management objective, but failed to define it. As a result, field biologists and managers have struggled to apply the concept to refuge management issues. Given this difficulty, I examined case studies of six northeastern National Wildlife Refuges to determine how biological integrity policy was incorporated into the Comprehensive Conservation Plan process mandated by NWRSIA, and how it has affected management decisions. I also examined how the “historical condition” aspect of biological integrity has affected management policy and practice, how refuges fit the presence of invasive species into models of historical condition, and how surrounding land use impacts managing for biological integrity. My analysis of how the biological integrity policy has been implemented reveals that its ambiguous definition hinders successful implementation at the refuge level. Few refuges identify biological integrity as a refuge goal in their CCP document. Developing a matrix or system of criteria to quantify and evaluate biological integrity would be a useful tool for refuge managers. Another recommendation would be to reassess the necessity of including “comparable to historical conditions” in the definition of biological integrity, as the phrase is misleading and creates an almost unachievable goal. The biological integrity policy is an important step towards unifying the vision of NWRs, but requires a practical translation for it to effectively contribute to refuge management.