We examined diel patterns in fish distribution, size and relative density in a side-channel of the River Garonne before and after a late-summer spate as part of a study of the role of floodplain wetlands in fish recruitment. Increases in fish size (SL) at night were mostly unaffected by the spate, whereas an increase in fish density at night, not observed prior to the spate, was observed in some species post spate. Microhabitat use was variable at dusk and night before and after the spate, but dawn and daytime microhabitat use were less variable after the spate. Water velocity, macrophytes and ligneous debris were the most important microhabitat variables prior to the spate, but were replaced thereafter by substratum composition and bank slope. Changes in microhabitat electivities were most apparent in abundant species, with shifts in depth, substratum and water velocity preferences in 0+ gudgeon Gobio gobio and 0+ chub Leuciscus cephalus. Our results indicate that habitat suitability (or preference) curves and electivity profiles are influenced by variations in river discharge, emphasizing the importance of using multiple samplings (diel, within-season, between-season) when setting habitat criteria for river management and when assessing the role of floodplain wetlands in fish recruitment.