A numerical model was developed to simulate water quality and algal species composition in a deep lake. As artificial destratification is widely used in the lakes, a destratification (bubble plume) model was incorporated with the ecological model to simulate the dynamic responses of different species under artificial mixing. The ecological model predicts concentrations of PO(4)-P, NH(4)-N, NO(3)-N, DO and pH throughout the water column, all of which have a significant influence on the growth of different algal species. The model has been calibrated using data from Uokiri Lake (Japan) for two different species (Diatom and Cyanobacteria) with and without artificial mixing. The calibrated model was used to simulate different conditions of artificial mixing within the lake over a period of five months. The simulation results show that artificial mixing favors non-motile heavier species, such as Diatom, while preventing the growth of Blue-green algae. It is also demonstrated that intermittent operation of the artificial mixing is better for water quality amelioration than continuous operation.