- Eutrophication of small prairie reservoirs presents a major challenge in water quality management and has led to a need for predictive water quality modeling. Studies are lacking in effectively integrating watershed models and reservoir models to explore nutrient dynamics and eutrophication pattern. A water quality model specific to small prairie water bodies is also desired in order to highlight key biogeochemical processes with an acceptable degree of parameterization. This study presents a Multi-level Watershed-Reservoir Modeling System (MWRMS) to simulate hydrological and biogeochemical processes in small prairie watersheds. It integrated a watershed model, a hydrodynamic model and an eutrophication model into a flexible modeling framework. It can comprehensively describe hydrological and biogeochemical processes across different spatial scales and effectively deal with the special drainage structure of small prairie watersheds. As a key component of MWRMS, a three-dimensional Willows Reservoir Eutrophication Model (WREM) is developed to addresses essential biogeochemical processes in prairie reservoirs and to generate 3D distributions of various water quality constituents; with a modest degree of parameterization, WREM is able to meet the limit of data availability that often confronts the modeling practices in small watersheds. MWRMS was applied to the Assiniboia Watershed in southern Saskatchewan, Canada. Extensive efforts of field work and lab analysis were undertaken to support model calibration and validation. MWRMS demonstrated its ability to reproduce the observed watershed water yield, reservoir water levels and temperatures, and concentrations of several water constituents. Results showed that the aquatic systems in the Assiniboia Watershed were nitrogen-limited and sediment flux played a crucial role in reservoir nutrient budget and dynamics. MWRMS can provide a broad context of decision support for water resources management and water quality protection in the prairie region.