Understanding the risks of planktonic algal proliferation and its environmental causes is crucial for protecting water quality and controlling ecological risks. Reservoirs, due to the characteristics of slow flow rates and long hydraulic retention times, are more prone to eutrophication and algal proliferation. Chlorophyll-a (Chl-a) serves as an indicator of planktonic algal biomass. Exploring the intricate interactions and driving mechanisms between Chl-a and the water environment, and the potential risks of algal blooms, is crucial for ensuring the ecological safety of reservoirs and the health of water users. This study focused on the Danjiangkou Reservoir (DJKR), the core water source of the Middle Route of the South-to-North Water Diversion Project of China (MRSNWDPC). The multivariate statistical methods and structural equation modeling were used to explore the relationships between chlorophyll-a (Chl-a) contents and water quality factors and understand the driving mechanisms affecting Chl-a variations. The Copula function and Bayesian theory were combined to analyze the risk of changes in Chl-a concentrations at Taocha (TC) station, which is the core water source intake point of the MRSNWDPC. The results showed that the factors driving planktonic algal proliferation were spatially heterogeneous. The main factors affecting Chl-a concentrations in Dan Reservoir (DR) were water physicochemical factors (water temperature, dissolved oxygen, pH value, and turbidity) with a total contribution rate of 60.18%, whereas those in Han Reservoir (HR) were nutrient factors (total nitrogen, total phosphorus, and ammonia nitrogen) with a total contribution rate of 73.58%. In TC, the main factors were water physicochemical factors (turbidity, pH, and water temperature) and nutrient factors (total phosphorus) with total contribution rates of 39.76% and 45.78%, respectively. When Chl-a concentrations in other areas of the DJKR ranged from the minimum to the uppermost quartile, the probabilities that Chl-a concentrations at the TC station exceeded 3.4 μg/L (the benchmark value of Chl-a for lakes in the central-eastern lake area of China) owing to the influence of these areas were all less than 10%. Thus, the risk of planktonic algal proliferation at the MRSNWDPC intake point is low. This study developed an integrated framework to investigate spatiotemporal changes in algal proliferation and their driving factors in reservoirs, which can be used to support water quality management in mega hydro projects.