Conservation of ecosystem engineers, which modulates the surrounding habitat by causing physical state changes in biotic or abiotic materials, is important for maintaining the functional integrity of ecosystems. This study examined the effects of endangered freshwater pearl mussels (Margaritifera laevis and M. togakushiensis) on channel morphology and flow in a low-gradient sandy river. For this, we performed a field removal experiment of mussels using three treatments in twelve 10-m reaches. Mussel abundance and biomass, and three physical variables were measured before, immediately after, and two months to one year after the treatments. Mussel removal resulted in channel degradation with a 60% increase in flow depth, a 30% decrease in current velocity, and a 50% reduction in the width-to-depth ratio two months after the treatments, whereas minimal changes were measured in reaches with mussels. The results indicated that pearl mussels act as an ecosystem engineer affecting the channel morphology and flow of sandy rivers.The conservation of the pearl mussel populations is key to preserving their far-reaching benefits in ecosystem integrity including habitats for other various organisms.