In this study, we compared the riverbed environment and benthic communities at the upstream and down-stream locations of two flow-through dams, the Nishinotani Dam and the Masudagawa Dam. No changes in the downstream riverbed caused by a decrease in the supply of coarse-grained sediment downstream of the Masudagawa Dam and the Nishinotani Dam were observed at this time. On the other hand, a decrease in the percentage of gravel was observed downstream of the Nishinotani Dam. The benthos community structure in the reservoir was differentiated from that in the control site, with an increase in the population of the Net-spinners type, a decrease in the population of the Gliders type, and an increase in the population of the Burrowers type due to gravel deposition, caused by decreased sediment mobility in the reservoir. The population of the Case-bearers type decreased downstream of the Nishinotani Dam due to the decrease in small gravel. On the other hand, no decrease in the number of Case-bearers was observed downstream of the Masudagawa Dam, where the downstream supply of small gravel is considered to be stable.