To identify the impact of a great flood event on phytoplankton assemblages and their succession in Gaozhou Reservoir, limnological variables and phytoplankton were investigated from January, 2010 to December, 2011. During flood, a mass of particles were flushed into the reservoir and overlaid the original surface sediment, which suppressed nutrients releasing from sediment. Nutrients concentration, especially phosphorus sharply decreased, and total phosphorus concentration was below 0.01 mg/L. After the flood event, the composition of suspended particles were changed, and water transparency decreased during the next mixing period because of the decreased resuspension of inorganic particles and phytoplankton biomass. The phytoplankton community structure rapidly responded to the significant change in the physical environmental variable. Dominant phytoplankton groups changed from colonial blue-green and large unicell Chlorophyta (Coda H₁ and N_A) to planktonic centric diatoms and dinoflagellates (Coda A, B and L_O). Anabaena mucosa which caused blooms yearly in every spring dry season could not be detected after the flood event.