Understanding the factors that govern the distribution of species is essential for their conservation. Over three years we quantified factors influencing habitat use by the common native Pacific tree frog, the threatened native California red-legged frog, and its invasive congener, the American bullfrog in forty ponds in central coastal California. We found strong differences in the tolerances of these species for poor water quality, degree of pond isolation, and proximity to habitat used by other amphibians. Water temperature, pH, proximity to roads and pond isolation all affect the distribution of endangered California red-legged frogs, although mount of agricultural runoff into a site and percent cover of a pond site with vegetation did not influence their distribution. Furthermore, the invasive American bullfrog shows none of these environmental constraints, allowing it to utilize a much wider range of habitat than its congener. In a dry year when there were few ephemeral breeding sites, the Pacific tree frog bred in the same ponds as larger frog species. But in years with higher rainfall, and hence more ephemeral breeding sites, tree frogs were strongly influenced by the distribution of other frogs, avoiding the permanent ponds they use. Studies such as these are critical for predicting which species may suffer declines first, and which of a constellation of human impacts are most critical in driving declines. They can also help with effective design of conservation and management strategies. With a strong grasp of how species use habitat, we can optimize conditions for species of concern and strive to make conditions unsuitable for invaders.