A three-dimensional numerical model was developed for simulating the concentration of water quality constituents. Four interacting systems were simulated, including phytoplankton dynamics, nitrogen cycle, phosphorus cycles, and dissolved oxygen balance. The effects of suspended and bed sediment on the water quality were also considered. The model was tested using analytical solutions for the transport of non-conservative substances in open channel flow, then calibrated and applied to a shallow oxbow lake to simulate the concentration of phytoplankton (as chlorophyll) and nutrients. The simulated trends and magnitudes of water quality constituents were generally in good agreement with field observations.