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Many aquatic species in the arid southwestern United States are imperiled, persisting primarily in isolated, low-order streams that are increasingly vulnerable to stochastic disturbances. During 2003 and 2004, we surveyed 39 mountain canyons in southeastern Arizona, USA, for lowland leopard frogs (Rana yavapaiensis), a species that has declined in abundance and distribution across its range in the United States. We quantified habitat features at 2 spatial scales, canyon and pool, to identify features that distinguished sites inhabited by frogs from those uninhabited by frogs. Canyons inhabited by frogs had watersheds that averaged 8.1 km(2) larger (SE = 2.52), pools that averaged 37.8 m(3) greater (9.30) in volume, gradients that averaged 4.1% (1.40%) less steep, and locations that averaged 3.2 km closer (1.06) to the nearest valley stream than did uninhabited canyons. Plunge pools inhabited by frogs averaged 13.5% (5.66%) more perimeter vegetation, 11.2% (5.34%) more canopy cover, and 1.9 (0.60) more refuges than uninhabited pools. In general, canyons that provided more perennial water during dry summer months and plunge pools that provided more bank heterogeneity were more likely to be inhabited by frogs. Conservation of lowland leopard frogs and other aquatic species that inhabit xeric systems in the southwestern United States depends principally on maintaining riparian ecosystems that provide habitat for these species and the adjacent uplands that influence the structure and function of these systems. Therefore, both riparian areas and their adjacent uplands must be managed to maintain habitat for organisms that inhabit these rare and diverse ecosystems.