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Fish are ubiquitous in pumped artificial drains but channel maintenance exposes fish to high flows and predators, and fish communities may experience population‐level threats if they are unable to access refuge during extreme flood‐relief pump operations. We assessed the impact of an extreme flood‐relief pump operation and effects of artificial habitat introduction on a resident fish community in an artificial drain in Great Britain using side‐scan and multi‐beam sonar. Sonar surveys before the flood found abundant aggregations of resident fish, whereas no fish were found after the flood, which suggested flood‐relief pump operations significantly altered resident fish populations. Fish abundance near artificial habitats monitored before the flood were highest during crepuscular periods and was similar among three different artificial habitat designs. Our findings improve the understanding of extreme flood impacts on fish in artificial drains and demonstrate the usefulness of sonar techniques for surveying abundance and spatial distribution of fish populations before and after floods.