Sedimentation in reservoirs is a major problem for sustainable water use, as it reduces flood control safety and water storage capacity. Meanwhile, stopping the sediment load of reservoirs leads to sediment depletion in the river channel below the dams and in the marine coast near the river mouth, which then severely affects on the health of the ecosystem. Several sediment control measures are being paid attention as a solution not only for sustainable water use but also for ecosystem restoration. Further studies are needed on the effects of sediment control measures on ecosystems. To control sedimentation, the three dams in the Mimi River, Japan have been operated together to implement sediment sluicing. We studied the effects of the sluicing operations on benthic macroinvertebrates in both river and marine ecosystems there. The taxa richness of freshwater macroinvertebrates increased at sites where large amounts of sediment were supplied by the sluicing operations. Most of the freshwater macroinvertebrates that appeared and increased after sediment supply were case builders, using inorganic materials like sand and gravel for portable cases and/or grazers, using periphyton as a food. The results of this study suggest that sediment supply would not only have direct effects, but also indirect ones via food resources in freshwater ecosystems. Following the sluicing operation with a huge flood, large amounts of sediment were supplied from the river to the estuary and coastal areas. Although the particle size distributions were very similar between the four stations we examined before the event, the differences in size distributions between them became apparent after one. Subsequently, sediment diversity increased in the marine environment, resulting in an increase in taxa richness of marine benthic invertebrates also increased. This study demonstrates that sediment supply is significant for maintaining the benthic macroinvertebrate diversity in both freshwater and marine ecosystems.