We compared densities of the caddisflies Ironoquia punctatissima (Walker) and Neophylax mitchelli (Carpenter) in microhabitats (cobbles, leaf litter, bedrock) nested within pool and run macrohabitats with different bedforms (stony [cobble-dominated] or flat bedrock) before and immediately after 4 floods in a north-central Ohio intermittent stream. Our goal was to identify which microhabitat and macrohabitat types acted as flow refugia. Ironoquia densities were highest on leaf litter in stony pools prior to floods. Flooding significantly lowered larval densities in stony and bedrock pools, where most leaf litter occurred, but not in runs. The most marked changes in pre- and postflood Ironoquia densities occurred in leaf litter, where densities decreased by ∼65 to 97% in 3 of 4 floods. In contrast, preflood densities of Neophylax were highest in bedrock runs and pools. However, floods significantly decreased Neophylax densities in these macrohabitats, suggesting bedrock macrohabitats provided larvae little shelter from high-flow forces. Measurement of cobble and leafpack tracer particles confirmed that hydraulic forces were highest in bedrock runs and that cobbles were far more stable than leaf packs in all macrohabitat types. Both species apparently face conflicting demands between residing in habitat patches that are food-rich but have poor flow refugia. Behavioral observations in a laboratory flume, where larvae were exposed to incrementally increased flows, revealed that Neophylax was more resistant than Ironoquia to dislodgment from cobbles and simulated bedrock, largely because of differences in body morphology and mass. These differences also partially explain why stony macrohabitats in the stream provided better flow refugia for Neophylax than for Ironoquia. Ironoquia, but not Neophylax, laid silk draglines, which helped prevent flow-induced dislodgment in low to moderate current speeds (≤0.4 m/s). Our study demonstrates how spatial attributes, scales, and species traits interact to determine or mediate flood effects on these caddisflies.