Schizothorax prenanti (S. prenanti) is a second-class provincial protected endemic fish within the upper reaches of the Min River. The spawning season of S. prenanti extends from March to April. Habitat alteration and the construction of multistage dams have resulted in a rapid decline of the S. prenanti population. To assess the potential effects of a reduced flow volume on the S. prenanti spawning habitat area in down- stream of dams, we combined River 2D and a habitat similarity evaluation model through the following steps. First, we conducted surveys of S. prenanti and the substrate composition in a natural habitat reach and a hydropower-affected reach. Second, hydraulic simulations were performed over a range of flows using River 2D. Third, vague sets of habitat variables were individually defined based on multi-expert opinions. Fourth, we estimated the weighted similarity of the S. prenanti spawning habitat using input variables (water depth, velocity) from River 2D. Fifth, we verified the model with S. prenanti survey data. Hydraulic simulations for velocity and depth yielded accuracies of approximately 84–97% and 81–98%, respectively. The weighted similarity simulations showed that weighted similarity increased with the flow up to a threshold range of approximately 130–150 m³/s; beyond this range, the weighted similarity decreased. The weighted similarity in the natural habitat reach was higher than in the restored reach at the same flow volume due to geography. The habitat similarity model provides restoration targets and thresholds for decision makers to develop a proactive conservation strategy for wetland management.