Waterfall plunge pools experience cycles of sediment aggradation and scour that modulate bedrock erosion, habitat availability, and hazard potential. We calculate sediment flux divergence to evaluate the conditions under which pools deposit and scour sediment by comparing the sediment transport capacities of waterfall plunge pools (Qsc_pool) and their adjacent river reaches (Qsc_river). Results show that pools fill with sediment at low river discharge because the waterfall jet is not strong enough to transport the supplied sediment load out of the pool. As discharge increases, the waterfall jet strengthens, allowing pools to transport sediment at greater rates than in adjacent river reaches. This causes sediment scour from pools and bar building at the downstream pool boundary. While pools may be partially emptied of sediment at modest discharge, floods with recurrence intervals >10 yr are typically required for pools to scour to bedrock. These results allow new constraints on paleodischarge estimates made from sediment deposited in plunge pool bars and suggest that bedrock erosion at waterfalls with plunge pools occurs during larger floods than in river reaches lacking waterfalls.