A vertically integrated hydrodynamic model (2-D) was firstly used to study the mechanism of the bloom in Fuchunjiang Reservoir. It proved that: (1) the morphological characteristic could indirectly influence on the aquatic ecosystem by directly deciding the spatial distribution of the flow regime of Fuchunjiang Reservoir. The section named Sandu Bridge where has wide lateral area is the accumulating region of algal biomass because of the low flow rate and intense internal nutrient flux to the euphotic zone. Moreover, influenced by the outflow position of the reservoir, a hydrodynamic convergence zone was formed and it would increase the chance of nutrient transfer from sediment to the euphotic zone. (2) The basin hydrological process indirectly influenced on the aquatic ecosystem by directly deciding the temporal distribution of the flow regime of Fuchunjiang Reservoir. The losing of algal biomass resulted from flushing was small so that algal biomass could remain at a high level in the year when the reservoir experienced a dry flood period (such as 2004 and 2007). Then, algal bloom would occur after flood period. But, the total algal biomass is low and bacillariophyta or cryptophyta would become the dominance population in the year when the reservoir experienced a wet flood period so that Fuchunjiang Reservoir could not form bloom easily.