As interest in ecosystems and the environment has recently increased, efforts for the preservation and restoration of river ecosystems have increased. The purpose of this study is to estimate the fish physical habitat by artificial change of streambed topography applying two-dimensional simulation model, River2D. A total reach length of 130 m along the Je stream located within the Geum River basin in Korea was used in this study. The target fish is the dominant fish species, Zacco platypus, which was evaluated for two growth steps (adult and spawning). Five scenarios were considered which included the installation of small dams at three different heights (0.25 m, 0.50 m, and 1.00 m) and installation of small pool with 0.25 m and 0.50 m depth. Results indicated that for natural streambed conditions the adult optimum flow was 1 m(3)/s, and the spawning optimum flow was 3 m(3)/s. The mean annual outflow for the natural condition was 0.64 m(3)/s, lower than the evaluated optimum flows. Applying the three discharges observed in 2008 to the five scenarios, the installation of the small dam increased the weighted usable area (WUA) while the installation of pools decreased the WUA, both as compared to the WUA for the natural condition.