This study attempted to analyze flow duration in a basin using a method to estimate environmental flow developed by the International Water Management Institute, and simulate the effects of runoff characteristics unique to a river and flow variability due to basin developments on aquatic ecosystems. To do so, KModSim, a simulation model for basin-wide water distribution, was used to assess flow duration in the Geum River basin, one of the four major river basins in Korea, by environmental management class (EMC). Flow duration curves by EMC at Sutong and Gongju sites were derived on the basis of natural flow in the Geum River basin. As a result, they were found to be consistent with the results of previous studies. Time series of mean monthly flow data by EMC were plotted together with those of simulated flow data by reservoir operation scenario; Sutong and Gongju points both showed flow behaviors corresponding almost to “A” in EMC. In addition, the characteristics of habitats by species of fish were identified through monitoring fish habitat at the Sutong site, so that optimal ecological flow rate was estimated. For this purpose, relations between flow discharge and weighted usable area for Coreoleuciscus splendidus and Pseudopungtungia nigra were projected using physical habitat simulation system, and EMCs consistent with flow duration curves (estimated taking in-stream flow) were assessed. The results or findings reported in this study are expected to serve as basic data for making a plan to efficiently monitor and manage aquatic ecosystems in the Geum River basin.