Environmental flows in the downstream sections of Yongdam Dam, Wonju Stream Dam, and Hongcheon River were estimated with selected target fish species such as Nigra for the site of Yongdam Dam, Splendidus for the site of Wonju Stream Dam, and Signifer for the site of Hongcheon River by considering endangered and domestic species. Physical habitat analysis was performed to estimate environmental flows for the study sites by applying the Physical Habitat Simulation (PHABSIM) and RIVER2D which combined hydraulic and habitat models. Based on the monitored data for ecological environment, the Habitat Suitability Index (HSI) for the target species was estimated by applying the Instream Flow and Aquatic Systems Group (IFASG). In particular, based on the result of fish monitoring, the HSI for each stage of the growth for target species was analyzed. As a result, the Weighted Usable Area (WUA) was maximized at 4.9 m3/s of flow discharge during spawning, 5.8 m3/s during the period of juvenile, and 8.9 m3/s during the adult fish season at the downstream section of Yongdam Dam. The result of the Wonju Stream Dam showed an optimal environmental flow of 0.4 m3/s, 1.0 m3/s, and 1.5 m3/s during the period of spawning, juvenile, and adult. The habitat analysis for the site of Hongcheon River, which is a non-regulated stream, produced an optimum environmental flow of 5 m3/s in the spawning period, 4 m3/s in the juvenile stage and 6 m3/s in the adult stage.