Protected areas around the world were created with the goals of preserving biodiversity and providing nature-based recreation opportunities for millions of people. This dual mandate guides the management of the majority of the world's protected areas, but there is growing evidence that quiet, nonconsumptive recreation may not be compatible with biodiversity protection. We combined noninvasive survey techniques and DNA verification of species identifications to survey for mammalian carnivores in 28 parks and preserves in northern California. Paired comparisons of neighboring protected areas with and without recreation revealed that the presence of dispersed, nonmotorized recreation led to a five-fold decline in the density of native carnivores and a substantial shift in community composition from native to nonnative species. Demand for recreation and nature-based tourism is forecasted to grow dramatically around the world, and our findings suggest a pressing need for new approaches to the designation and management of protected areas.