Despite the prevalence and importance of intermittent streams, few studies have examined their use by crayfishes. We documented persistence in an intermittent stream and use of the hyporheic zone by 2 imperiled crayfishes, Orconectes williamsi and Orconectes meeki meeki, upon stream drying. During 2005 to 2007, we monitored summer flows and crayfish densities in 10 riffles in a Missouri (US) Ozark stream to document stream drying and crayfish persistence. Stream drying variables were riffle wetted area (m²) and current velocity (m/s). Crayfish density estimates were obtained with a quadrat sampler. We sampled monthly (May–August 2006) to examine crayfish response to decreased flows, and excavated dry quadrat samples (to 30 cm depth) after surface flows ceased. Over 2 periods during summer 2007, we used baited traps in the stream and a downstream reservoir where the stream terminates to examine whether crayfish migrated from the stream to permanent water in response to drying. Riffles dried significantly by July, few had surface water present by August, and all were rewetted by the following June. Annual June densities of O. williamsi remained stable throughout the study, whereas densities of O. m. meeki were lower in 2007 than 2005. Both species burrowed to the hyporheic zone during drying, and crayfish densities were similar to those estimated in riffles before drying. We found no evidence that either species migrated to permanent water in the reservoir during drying. Use by crayfish of the hyporheic zone during drying and interannual persistence in intermittent streams suggests that hyporheic habitats are important for conservation of these crayfishes. Our study contributes to the increasing body of knowledge that indicates the importance of intermittent streams for conservation of freshwater biodiversity.