An algal bloom is a complex hydro-biological phenomenon driven by multi-attribute environmental processes and thus is still difficult to predict. In this paper, a comprehensive modelling framework for forecasting algal bloom risks in shallow lakes is presented, which is based on long-term field observation and modelling of eutrophic shallow lakes. In the procedure, the major factors and their suitable ranges are investigated, and the individual influence of various driving factors is evaluated quantitatively, using an integrated approach of orthogonal design and regression analysis. By analyzing the possible combined effects of the major driving factors and the relationship between algal bloom risk and major bloom-driving factors, a cost-effective environmentally driven risk assessment model is developed to forecast the likelihood of algal bloom occurrence, through a parameter optimization and prediction comparison routine. The risk model has been calibrated and validated against long-term field observations of algal blooms in Taihu Lake, with the prediction accuracy higher than 70%, which only requires readily available meteorological and water quality data. It is noted that for the closed shallow lake, the influence of hydrodynamics can be indirectly reflected by the variation of wind speed; and, TP, water temperature (WT), photosynthetically active radiation (PAR), and average wind speed (AWS) could be used as major bloom-driving factors in Taihu Lake generally. This study provides a practical framework for the development of algal bloom early warning schemes for shallow lakes and helps to understand the combined function of complex bloom-driving factors.