Nutrient cycling flux in lakes is an important indicator to measure the lake trophic state as well as an essential approach to explore eutrophication mechanisms. Key processes of nutrient cycling can be identified by calculating nutrient cycling fluxes and mass balance analysis. In this study, IWIND-LR, a 3D hydrodynamic and water quality model, was used to simulate nutrient cycling of lakes in this study. The nutrient cycling fluxes were calculated based on the model results to define the contributions and patterns of nutrient source and sink processes. Lake Dianchi in the Yunnan Plateau is one of the most severely polluted lakes in China. It is a semi-closed lake and provides a stable environment for research. The model results demonstrated that, IWIND-LR performed well in Lake Dianchi. The input and output of total nitrogen in Lake Dianchi was 7620.92 t and 7637.31 t respectively in 2003; while 450.23 t and 429.57 t for total phosphorus. The exogenous loading contributed most of the input of nitrogen and phosphorus, while denitrification and sedimentation were the major outputs of Lake Dianchi.