Often land set aside for conservation becomes a multiple use area, which forces land managers to balance biodiversity values against competing needs. Booderee National Park is an important conservation reserve for a range of amphibian species in south-eastern Australia. The Park includes a number of townships, defence facilities, and recreation areas, as well as land for conservation. We examined amphibian communities in the area and related these to broad habitat features and identified potential threats to the long term viability of these populations. Two distinct assemblages occurred within the Park that could be related to broad habitat features of the breeding site (i.e., wet heath and open water wetlands). There are three potential threats to the viability of these populations: (1) inappropriate fire regimes; (2) introduced predators; and (3) infection by the chytrid fungus. While fire regimes and predators can be managed, the chytrid fungus cannot and therefore represents the primary concern for amphibians in the area.