Entrainment and mortality of freshwater fish at hazardous pumping station intakes used for Flood Risk Management (FRM) are of global concern. Although upstream and downstream passage of diadromous fish has received considerable attention, the ecological behaviours of river-resident fish at these structures and how to protect these species from entrainment is poorly-understood. At a lowland flood-relief pumping station and floodgate situated off-channel (River Foss) to the main-river Yorkshire Ouse (York, England), multi-beam sonar (Dual-Frequency Identification Sonar: DIDSON) was used over a pluriannual (three years) period to investigate diel movements of river-resident fish in response to the variations in temperature, hydrology and pump and floodgate operation, and to determine fish-friendly management options. Diel lateral movements of thousands of river-resident fish between the main-river, floodgate operated channel (River Foss) and off-channel pump forebay were predominantly during the crepuscular period and daytime, proposing important considerations for when managers should operate pumps and associated flood infrastructure. Seasonal diel movements increased throughout winter during a baseline year (no pump operation) and overwintering behaviour was influenced by cooling river temperatures. A Generalized Linear Mixed Model (GLMM) revealed fish entered the off-channel forebay when river levels were stable and not when they were rising or falling, suggesting hydrological stability was important for the ecological function of this fish community. Two years of impact data (pumps operated) then revealed pump operations severely disrupted the ecological functions of local fish populations, which was also uniquely quantified over two independent 24h periods during which temporal fish counts were reduced by 85%. A trial period where the floodgate was lowered ahead of dawn significantly reduced fish immigration into the hazardous forebay when compared to two different hydrological periods. Modifying when the floodgate and pumps operate, including lowering the floodgate ahead of fish immigration at dawn, and starting pumps during the night (but not day), are therefore promising non-engineered management options to prevent immigration of fish into the hazardous off-channel pump forebay and to reduce entrainment and mortality risk during pump operation.
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