Ecological flow (E-flow) determination is an essential component of stream management and the preservation of aquatic ecosystems within a watershed. E-flow should be determined while considering the overall status of the watershed, including the hydrological cycle, hydraulic facility operation, and stream ecology. The purpose of this study is to determine E-flow by considering watershed status through coupled modeling with SWAT and PHABSIM. SWAT was calibrated to ensure reliability when coupling the two models, using observed data that included streamflow and dam inflows. The calibration result of SWAT showed that the averages of R2, NSE, and RMSE were 0.62, 0.57, and 1.68 mm/day, respectively, showing satisfactory results. Flow duration analysis using the SWAT results was performed to apply to discharge boundary conditions for PHABSIM. The averages of Q185 (mid-range flows) and Q275 (dry conditions) were suitable to simulate fish habitat. The habitat suitability index derived through a fish survey was applied to PHABSIM to estimate E-flow. E-flow was estimated at 20.0 m3/s using the coupled model and compared with the notified instream flow by the Ministry of Environment. The results demonstrate a high level of applicability for the coupled modeling approach between the watershed and physical habitat simulation models. Our attempt at coupled modeling can be utilized to determine E-flow considering the watershed status.