Flushing is a common measure to manage and reduce the amount of sediment stored in reservoirs. However, the sudden release of large volumes of sediment abruptly increases the suspended solids concentration and alters the riverbed composition. Similar effects can be produced also by natural flood events. Do flushing operations have more detrimental impacts than natural floods? To answer this question, we investigated the impact of flushing on the survival of the Chinook salmon (Oncorhynchus tshawytscha) in the Sandy River (OR, USA), assuming that sediment is flushed from hypothetical bottom gates of the, now decommissioned, Marmot Dam. The effects of several flushing scenarios are analyzed with a 2D morphodynamic model, together with habitat suitability curves and stress indicators. The results show that attention has to be paid to duration: the shorter the flushing operation, the lesser the stresses on fish survival and spawning habitats. Flushing causes high stress to salmon eggs and larvae, due to unbearable levels of suspended sediment concentrations. It also decreases the areas usable for spawning due to fine-sediment deposition, with up to 95% loss at peak flow. Without the dam, the corresponding natural flood event would produce similar effects, with up to 93% loss. The study shows that well-planned flushing operations could mimic a natural impact, but only partly. In the long-term, larger losses of spawning grounds can be expected, since the removal of fine sediment with the release of clear water from the reservoir is a lengthy process that may be undesirable due to water storage reduction.