The ecohydraulic modeling framework in ecological systems includes hydro-morphodynamic, habitat, and population models. In this paper, we proposed an ecohydraulic modeling framework that combines numerical methods and ecological theories to explore the dynamics and interplay between fluvial processes in rivers and the quality of physical habitat and density distribution for fish. The practicality of applying the developed system to ecohydraulics modeling was explored through three case studies and compared with as well as validated using observed data. On the basis of the calculated results, the model system was proven to be efficient in describing population dynamics of the European grayling (Thymallus thymallus. L.) in the Aare River in Switzerland. Satisfactory predictions of the long-term population evolution of the rainbow trout (Oncorhynchus mykiss), brown trout (Salmo trutta) and flannelmouth sucker (Catostomus latipinnis) in the Colorado River in the United States (US) were obtained. Furthermore, the effects of Da-Wei Power Plant construction on the Jiao-Mu River in China on the schizothorax (Schizothorax prenanti) and schizothorax (Racoma) fish species were investigated. The efficiency of fish stocking strategies was evaluated and optimal fish stocking numbers were proposed. The resulting ecohydraulic modeling framework provided very promising results, which highlighted the fundamental role of the temporal variability of hydro-morphological parameters in structuring populations of fish species. Using the ecohydraulic modeling framework to simulate population trends in anticipation of any changes in water management can provide decision-makers with valuable prediction results.