Floods are often considered one of the major regulators of fish populations, but there are few observations of fish behaviour or habitat use at such times. To investigate habitat use and fish movement during floods, two locations on the Pohangina River, North Island, were sampled at the peak of a small flood. Habitat use at normal flows was determined by repeating the same sampling procedure in runs and riffles on the Pohangina and two nearby rivers. The sampling procedure was to electrofish runs and riffles in lanes, stratified by depth (0–0.125 m, 0.125–0.25 m, 0.25–0.5 m, and 0.5–0.75 m). Water depths and velocities were measured in each sampling lane. Fish were most abundant along the river margins less than 0.25 m deep, both during the flood and in normal flows. Two days after the flood, these shallow areas, that had been occupied by fish during the flood, were dry again. This suggests that the edge‐dwelling fish species in these rivers respond quickly to flow changes, moving with the river margins to minimise any change in depth. Response to changes in velocity were less apparent and the water velocity in the areas occupied by edge‐dwelling fish during the flood was sub‐optimal in terms of normal habitat preference. The response of fish to flow and habitat change and the use of sub‐optimal habitat for short periods of time highlights the difficulty of interpreting a time series of weighted usable area.