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Flood disturbance plays a key but complex role in structuring lotic ecosystems. Empirical models proposed here allow salmonid resource managers to quantify the probability of egg pocket scour during floods and to predict how the expected losses vary with flood strength and reach characteristics. The models are based on comparisons between published salmonid egg pocket depth criteria and statistics on the intensity and spatial distribution of scour and fill produced by three flood events of widely different magnitudes in three separate reaches of a gravel-cobble Atlantic salmon (Salmo salar) river in the Saguenay region, Quebec. A simple substrate mobility index, based on reach-scale geomorphic characteristics and flood hydraulics, was shown to provide useful predictions (R2 up to 74%) of the fraction of the area of potential spawning zones undergoing flood scour greater than 30 cm. Any Atlantic salmon egg pockets present in these deeply scoured areas would be destroyed. The models also predict the distribution of fill (net rise in bed) potentially causing fry entombment at redds. The flood disturbance data suggest that average probability of scour of an Atlantic salmon egg pocket in the study reaches ranges from under 5% for frequent-recurrence spring floods to approximately 20% for an extreme, multicentenary-recurrence flood.