This study presents the impact of natural flow patterns on downstream aquatic species habitats in a reach of the Geum River, Korea. The study reach is a 13.4 km long, located downstream of the Yongdam Dam. To assess such an impact, this study performed physical habitat simulations. The River2D model was used for the computation of the flow field and morphology, and the Habitat Suitability Index (HSI) model for the habitat simulation. Three habitat variables-flow depth, velocity, and substrate were used. The Zacco platypus and Baetis fuscatus were selected as the target fish and benthic macro-invertebrate, respectively. Using the building block approach (BBA), the scenarios for modifying dam operations were constructed in the study reach. Scenario 1, scenario 2, and scenario 3 were proposed by using the magnitude-duration concept, base flow allocation concept, and seasonally adjusted minimum flow allocation concept, respectively. Simulation results indicated that the scenarios' effects significantly increased by about 14.3% for the weighted usable area (WUA). In addition, the morphology change with the restoration of flood events was investigated. It was revealed that the morphology change in the physical habitat simulations further increased by about 13% for the WUA. The change of dam operations through natural flow patterns is more advantageous to aquatic species.