Flow-dependent microhabitat use by brown trout: insights from PIT telemetry

Abstract Understanding stream fish habitat use in response to hydrological variability is key for effective riverine management under increasing climate-induced flow extremes. In this field study, we investigated microhabitat use by brown trout ( Salmo trutta Linnaeus, 1758) in a Central European low mountain stream using PIT telemetry over three years. Continuous monitoring captured habitat preferences under low, moderate, and high-flow conditions. During low flows, trout mainly used riffles with stable, coarse substrates, while juveniles occupied more cryptic refuges. At moderate discharge, detection rates across age groups converged, suggesting more uniform habitat use, possibly due to greater accessibility or reduced spatial constraints. Under high-flow conditions, trout retreated to deeper pools offering structural cover such as woody debris and undercut banks, likely reducing energy expenditure and predation risk. Juvenile detections were particularly scarce when discharge reached the uppermost high-flow range, possibly reflecting displacement, reduced swimming capacity, or use of refuges beyond detection range. Our findings highlight the need to preserve a mosaic of habitat types, including riffles, pools and complex cover, to support age-specific responses and enhance trout resilience under hydrological extremes. This study underscores the value of long-term in situ data for informing conservation strategies in dynamic freshwater ecosystems.