The Refuge Improvement Act of 1997 established a statutory mission and management standards for the National Wildlife Refuge system. The U.S. Fish and Wildlife Service subsequently issued a policy for ensuring the biological integrity, diversity, and environmental health of the system. This policy requires understanding the management objectives of each refuge in a local, regional, and national context. An assessment of the refuge system in a national and regional context reveals that refuges are typically smaller than many conservation holdings and are unevenly distributed across the conterminous U.S. Western rangelands, coastal wetlands, and northern grasslands; wetlands are the best-represented ecosystems, while temperate forests have the poorest representation. In contrast to other agency holdings or management designations in the national protected areas network (e.g., national parks, national forests, wilderness areas), refuges tend to occupy sites at lower elevations and that have higher productivity and soil quality. This difference points to the important contribution of the refuges in providing much needed ecological balance within the national protected areas network. However, the ecological integrity of the refuge system is challenged by the proximity of individual refuges to development. Overall, the refuges are becoming islands in a landscape matrix of urban and agricultural development. This creates future challenges for meeting management objectives to ensure the biological integrity, diversity, and environmental health of the system. If the policy to ensure biological integrity, diversity, and environmental health of the refuge system is to be successful, it may be more important to address issues about what happens on adjacent lands than uses within refuges.