Flooding is an important physical disturbance in many streams and rivers. Ecological theory suggests that population persistence will be enhanced if organisms can take shelter from high flow during floods. We investigated whether the black fly larva Simulium tribulatum actively moves to sheltered microhabitats during natural and simulated floods. First, we quantified the relationship between larval abundance and availability of sheltered and exposed microhabitats on a single boulder during and after a natural flood in Taylor Run, Pennsylvania. Changes in abundance were significantly associated with microhabitat type. Abundances in all sheltered microhabitats were greater during than after the flood, whereas abundances in all exposed microhabitats were lower during than after the flood. We used a controlled field experiment to verify this relationship by creating simulated floods over artificial substrata containing exposed and sheltered microhabitats. Larval densities were highest in exposed microhabitats before and after the flood, but were highest in sheltered microhabitats during the flood. Larval densities on constant-flow substrata were always highest in exposed microhabitats. We used hotfilm anemometry in a laboratory flume to quantify near-bed velocities in different microhabitats on an artificial substratum during low- and high-velocity conditions, and examined corresponding changes in larval density in those microhabitats. During high-velocity conditions, larval densities declined in microhabitats with near-bed velocities >100 cm/s and increased in sheltered regions with velocities <100 cm/s. Thus, larvae can move quickly to sheltered microhabitats as velocities increase, and return rapidly (order of minutes) to more exposed microhabitats as velocities diminish. This behavior should confer fitness benefits and enhance population persistence, particularly in streams with larger substratum sizes that remain immobile during most floods.