Ephemeral streams in the southwestern United States have unpredictable, short, torrential flows during extreme weather, and their aquatic biology is poorly studied. During the 2006 monsoon, we sampled aquatic communities at 14 ephemeral stream sites within the Santa Cruz River, Arizona, and Río Puerco, New Mexico, watersheds following a monsoon-related thunderstorm and continuing daily until flows and pools dried. With the 86 taxa of macroinvertebrates that we collected, these sites host a modest community, although presence was limited by drying. Macroinvertebrate taxa richness was not associated with duration of water presence, and biomass was greater in sites with less water available. We collected more taxa in ephemeral reaches of interrupted streams than in truly ephemeral streams. Drought-resistant/resilient species traits were well represented. Vertebrates colonized these ephemeral stream reaches quickly; however, native fish species used ephemeral reaches as corridors between perennial reaches while nonnative fish were unable to do so, and amphibians sometimes completed the aquatic portion of their life cycle in the receding waters. This study provides the first data on aquatic organisms in ephemeral streams immediately after monsoon thunderstorms in the southwestern United States.