The longitudinal continuity of communities is an important issue in rivers. The fishway at the Miyanaka Intake Dam in the middle reach of the Shinano River was re-constructed. In addition to the traditional fish ladder, a nature-like fishway was newly constructed. Experimental flushing was conducted. The monitoring results before and after the flushing indicated that there was not much impact on the composition of benthic flora and fauna, although benthic materials and benthic algae were sufficiently cleansed. Monitoring of fish species and macroinvertebrates composition indicated that it was extremely effective for organisms with low swimming ability, such as demersal fish and benthic macroinvertebrates.