A water transfer project has been ongoing since 2002 to alleviate severe phytoplankton aggregation in Lake Taihu. This study aimed to quantify the effectiveness of the water transfer project on alleviation of phytoplankton aggregation in Lake Taihu on a short-term scale. In this study, a spatially distributed hydrodynamic-phytoplankton model was used to predict the short-term (3–4 days) changes in phytoplankton distribution (represented by chlorophyll a) in Lake Taihu. Four simulations with different water transfer strategies were carried out based on this model. During the water transfer period, phytoplankton aggregation was alleviated in some areas, suggesting that the water transfer project has the potential to alleviate algal blooms on a short-term scale. However, the effectiveness of the water transfer project on alleviating severe algal blooms was strongly affected by other environmental factors (e.g. wind conditions, chlorophyll a distribution, and the amount and quality of the transfer water). This study demonstrates the success of the hydrodynamic-phytoplankton model in evaluating the contribution of the water transfer project to alleviation of phytoplankton aggregation. These evaluation results could assist managers in decision-making before conducting a water transfer plan in Lake Taihu.