1. Flow intermittence is a major disturbance for riverine fishes. Many species of fishes that evolved in naturally intermittent streams have specialized adaptations to survive drought such as movement to refuge habitats. Conservation of fishes in river systems with highly altered flow regimes requires understanding of how individuals and populations respond to flow intermittence.2. Here, flow was manipulated in two 16-km segments of the Rio Grande, New Mexico, to determine whether managed flow recession could reduce stranding imperilled Rio Grande silvery minnow in isolated pools.3. Slower flow recessions did not decrease stranding in isolated pools over the range tested. Flow recession rate appeared to have an adverse impact on stranding; fewer fish were stranded under faster recession rates, but complex interactions were evident. Fish were stranded throughout both segments regardless of flow recession rate.4. No evidence of a synchronized movement response was observed. Instead, many Rio Grande silvery minnows were probably trapped within proximal habitats, which dry completely and function as evolutionary traps, rather than moving to areas of perennial flow. Use of proximal habitats during streamflow intermittence has implications for management of the species and mitigation of mortality, including managed flow recession rates, and position and function of refuge habitats.5. Effective mitigation for flow intermittence and stranding in streams with highly modified flow regimes will depend on the life history and behavioural response of the species. For Rio Grande silvery minnow, facilitating adaptive behaviour would require creating refuge areas that increase fish survival for weeks to months, as reducing the attractiveness of the traps is likely to be impossible given lack of a synchronized movement response to declining flows. Mismatching life-history strategies, behaviour, and scale of conservation actions may result in ineffective