Amphibians present a particularly complex conservation challenge due to their biphasic lifecycle (i.e., aquatic larvae and terrestrial adults), in which successful reproduction depends on the quality of multiple habitats that must co-occur in time and space. In a highly dynamic, arid system such as the Sonoran Desert, the alignment of terrestrial habitat conducive to adult activity and aquatic habitat suitable for larvae may occur only within a small window. Here, the water sites required for larval development are rare islands on a dry landscape and the monsoonal rains that provide moisture for terrestrial adult activity are extremely stochastic both spatially and temporally. Furthermore, as the climate changes, the timing and volume of monsoonal rains are expected to shift, and with it the timing and availability of breeding habitat for amphibians. Further altering their breeding resources, constructed waters have been built throughout the region to increase water availability for wildlife; however, these sites differ from natural sites in their structure and water chemistry and may not always provide quality larval habitat. As the impacts of climate change and water management practices alter the quality and timing of breeding resources for amphibians in the Sonoran Desert, identifying important habitat characteristics for adult breeding effort and tadpole occurrence may be vital to future conservation of populations. To investigate features of desert waters related to patterns of adult occurrence, breeding effort, and breeding success, we sampled waters in southwestern Arizona for amphibians in five years using visual, acoustic, and dip-net survey methods and implemented a multi-state occupancy model. We found higher probabilities of adult occurrence and breeding effort at natural water sites compared to constructed waters. Breeding effort was also more likely to occur with more precipitation, and the probability of breeding success increased with higher breeding effort. Thus, actions that target and protect natural water sites may be vital to support adult breeding effort, and thereby breeding success, to bolster amphibian conservation in arid lands through the impacts of climate change.