Nakagawa experimental forest of Hokkaido University is located in the middle Teshio River and some tributaries flow through the forest. The construction of Otoineppu bypass route started in 2007. This bypass route will passes through the forest. In order to evaluate the impacts of the road construction on stream ecosystem, a long-term monitoring of fish community and stream environmental characteristics have been conducted including before, during and after the road construction. The survey has been implemented on five streams in Teshio River (three streams inside the bypass construction zone and two streams outside the zone). Here, we report the data of species, body size and body weight of fish sampled using an electrofishing unit and the data of stream environmental characteristics such as water temperature, water surface area, pH, and EC. The three-pass removal method for fish sampling and measurement of stream environmental characteristics were conducted three times a year (mainly June, August and October) from 1999 to 2018. A total of 57,203 individuals were observed, belonging to 11 species in 7 families. After bypass road construction started (2007), the number of fishes gradually increased at both of bypass road construction and control sites. Occasionally, the number of fishes at the bypass construction site tended to be lower than at the control site, but there was not always noticeable difference between them. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in Ecological Research Data Paper Archives at http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/archives/2020/ERDP-2020-09.