Artificial changes of rivers, including construction and operation of dams, inevitably lead to physical and ecological changes throughout waterways and their floodplains. In this study, a conceptual model coupled with integrated numerical modeling is presented for hydraulic fish habitat assessment of the Geum River basin, Republic of Korea. Based on the major events which might have affected the ecological system, a conceptual model was formulated to guide desktop and field studies, modeling and scenario evaluations. The result of hydraulic fish habitat assessment indicated that the construction of the Daecheong Multipurpose Dam (DMD) in the Geum River basin has altered flow magnitudes and reduced the river's flow variability. Changes are evident in the magnitude of medium and small flows and the river experiences increased low flows during the dry season. Black shiner, an endangered fish species in Korea, was selected and analyzed to explore relationships between flow regime change by dams and changes to its preferred habitats. As a result, fewer sensitive riffle-benthic species were observed in the reaches downstream of DMD due to the reduction of suitable habitat conditions such as riffle-pool sequences. The proposed conceptual model and integrated toolkit would allow river managers to isolate the physical and biological effects associated with dam operation and could be useful for developing river management strategies.