Natural rock pools, tinajas, and constructed catchments in the Sonoran Desert provide water for a wide variety of organisms. In 2012, we monitored water quality and amphibian and dragonfly use of wildlife waters in southwestern Arizona, USA. We measured ammonia concentrations that exceeded the U.S. Environmental Protection Agency's guidelines for aquatic life and were well above concentrations that cause mortality in amphibians and other aquatic organisms. Both amphibians and dragonflies had lower species richness in catchments than in the tinajas, and amphibian species richness was negatively associated with ammonia concentration. These concentrations of ammonia alone cause concern for the management of biodiversity, specifically for wetland-dependent organisms. Furthermore, ammonia concentrations may be high enough to impact terrestrial organisms of economic and conservation importance including humans. © 2013 The Wildlife Society.