Aquatic diversity in the arid Southwest is sustained by thousands of small ponds and wetlands, many of which are ephemeral. The maintenance of taxonomic and functional diversity across this system therefore depends on how well taxa can either survive drying events or disperse across the landscape to reestablish their populations. To track changing ephemerality, connectivity, and biodiversity through >5 years of drought conditions our lab has combined remote sensing and community sampling in nearly 50 ponds. Remote sensing using Sentinel-2 imagery revealed a consistent decrease in habitat availability in the early summer period between snowmelt and the monsoon season. Despite this frequent drying, many ephemeral and permanent ponds support equivalently diverse communities, each with distinct specialists, such as fairy shrimp in ephemeral ponds and amphipods in permanent ponds. Drying events in ponds without a history of disturbance can shift communities into a lower diversity state dominated by generalists, but recolonization by generalists is remarkably fast, with no evidence for dispersal limitation. In the absence of specialists, diversity appears to depend not on connectivity or hydroperiod but on habitat quality indicators such as submerged aquatic vegetation and turbidity, which can be impacted by invasive species and land management. Together, these studies show that climate effects on macroinvertebrate diversity depend on the traits of the original species pool as well as interactions with other global change stressors.