Despite the progress in three-dimensional (3D) hydrodynamic, water quality, and sediment diagenesis models and their successful applications in estuaries and bays, few similar 3D modeling studies on lakes and reservoirs have been published. In this study, a 3D hydrodynamic and water quality model has been developed and applied to Lake Tenkiller, Oklahoma. The model includes coupled hydrodynamic, eutrophication, and sediment diagenesis processes. Lake Tenkiller is a manmade reservoir up to 45 meters deep. The lake measures 48 kilometers (km) long, up to 3 in wide, and 70 km(2) in area. Its major water quality issues include nutrient enrichment, eutrophication, and hypolimnetic oxygen depletion. With large lateral variations, the lake needs a 3D model to simulate the hydrodynamic and water quality processes in detail. The model has 198 horizontal grid cells and 10 vertical layers. Measured data at 14 stations from February 1986 to September 1986 are available for hydrodynamic and water quality model calibration, including water elevation, water temperature, dissolved oxygen, chlorophyll a, 5-day biochemical oxygen demand, orthophosphorus, and nitrate-nitrogen. Comparisons between the modeled results and the measured data for all parameters were satisfactory. Seasonal variations of water quality variables in the lake were well replicated. A series of test cases was conducted to illustrate the importance of 3D modeling of lake hydrodynamic and eutrophication processes. It is shown that lake stratification and wind forcing are two major hydrodynamic processes controlling the hypolimnetic oxygen depletion. A seiche signal with a period of 2.36 hours is found in the lake. Theoretical estimation, time series plots, and the Fourier analysis all consistently support this finding. The model is used as a tool for water quality management in the lake.