It is widely recognized that high supplies of fine sediment, largely sand, can negatively impact the aquatic habitat quality of gravel-bed rivers, but effects of the style of input (chronic vs. pulsed) have not been examined quantitatively. We hypothesize that a continuous (i.e. chronic) supply of sand will be more detrimental to the quality of aquatic habitat than an instantaneous sand pulse equal to the integrated volume of the chronic supply. We investigate this issue by applying a two-dimensional numerical model to a 1 km long reach of prime salmonid spawning habitat in central Idaho. Results show that in both supply scenarios, sand moves through the study reach as bed load, and that both the movement and depth of sand on the streambed mirrors the hydrograph of this snowmelt-dominated river. Predictions indicate greater and more persistent mortality of salmonid embryos under chronic supplies than pulse inputs, supporting our hypothesis. However, predicted mortality varies both with salmonid species and location of spawning.We found that the greatest impacts occur closer to the location of the sand input under both supply scenarios. Results also suggest that reach-scale morphology may modulate the impact of sand loads, and that under conditions of high sand loading climaterelated increases in flow magnitude could increase embryo mortality through sand deposition, rather than streambed scour.