A dynamic three-dimensional water quality model for macrophyte-dominated shallow lakes was proposed and tested. The proposed model is capable of simulating macrophytes and its interactions with water quality constituents such as dissolved oxygen (DO), organic nitrogen, ammonia, nitrate, organic phosphorus, orthophosphate, biochemical oxygen demand, phytoplankton and the sediment layer in shallow lakes. An existing two-dimensional hydrodynamic model has been utilized in conjunction with the water quality model to simulate water levels, velocities and flow rates. The modelled macrophyte processes are photosynthesis, respiration, mortality and excretion. Hourly simulation of photosynthesis process has been realized. The hourly simulations need special attention to predict diurnal variations of DO in macrophyte dominated lakes. The proposed water quality simulation model was subjected to calibration, verification and prediction processes using the data collected from Mogan Lake, Turkey. Mogan Lake exhibits wide variations of macrophyte biomass seasonally. The lake also exhibits highly variable DO levels both seasonally and diurnally. Statistical error quantification methods have been utilized to test the goodness of fit between the water quality model predictions and field measurements. Good agreement has been achieved between model predictions and measurements. Moreover, uncertainty analysis has been carried out for macrophyte and DO constituents. The analysis showed that the magnitude of the saturated growth rate of macrophyte is the most sensitive model parameter both for macrophyte and DO. The proposed water quality simulation model gave some promising initial results as a management tool to predict the expected reductions for the undesired consequences of eutrophication problem. (C) 2000 Elsevier Science B.V. All rights reserved.