Based on a 2-D hydrodynamic model, a vertically integrated eutrophication model was developed. The physical sub-model can be used for calculation of water density at different depths, and the water quality sub-model was used for calculation of algal growth. The cohesive and non-cohesive sediments were simulated separately with different methods. The light extinction coefficient used in the underwater light regime sub-model was linearly related to the sum of sediment and phytoplankton biomass. Some components less important to the model were simplified to improve practicability and calculation efficiency. Using field data from Fuchunjiang Reservoir, we calculated the sensitivity of ecological parameters included in this model and validated the model. The results of sensitivity analysis showed that the parameters strongly influenced the phytoplankton biomass, including phytoplankton maximum growth rate, respiration rate, non-predatory mortality rate, settling rate, zooplankton maximum filtration rate, specific extinction coefficient for suspended solids and sediment oxygen demand rate. The model was calibrated by adjusting these parameters. Total chlorophyll a (chl-a) concentrations at different layers in the water column were reproduced very well by the model simulations. The simulated chl-a values were positively correlated to the measured values with Pearson correlation coefficient of 0.92. The mean difference between measured and simulated chl-a concentrations was 12% of the measured chl-a concentration. Measured and simulated DO concentrations were also positively correlated (r = 0.74) and the mean difference was 4% of measured DO concentrations. The successful validation of model indicated that it would be very useful in water quality management and algal bloom prediction in Fuchunjiang Reservoir and a good tool for water quality regulation of other river-style reservoirs.