In this paper, an improved simulation method was developed to investigate the mechanisms of algal growth in Poyang Lake, which is the largest freshwater lake and the most typical river-connected lake in China. In view of its frequent water and sediment exchange with the external rivers, the influences of flow disturbance and suspended sediment concentration on algal growth were quantitatively analyzed based on field investigation and laboratory experiment, and the controlling equations of l(u) and g(S) were established and embedded into the traditional algal growth model for more accurate simulation in Poyang Lake. The improved model was calibrated and validated against the consecutive field monitoring data from March to November in 2012. By simulation, the algal concentration fluctuation in a common-water year and the spatial distribution under two typical current structures: “Gravity Style” and “Jacking Style,” were quantitatively estimated. The results showed that the improved model gave a good approximation of the algal growth processes under the varied water–sediment environment in Poyang Lake. Algal concentrations in the middle area were evidently higher than that in the south and north lake area, while the variation trends were basically the same. Due to the slower current, the algal concentration under “Jacking Style” flow structure was averagely increased by 18.8 % than that under the “Gravity Style.”