Shallow dished lakes, isolated bays and the main water body of Poyang Lake were studied during common water period, flood period and drought period. The water, phytoplankton and dissolved microcystin samples were collected and analyzed. Results showed that in all periods, water quality and algae population varied greatly among the three areas. Dissolved microcystin concentration correlated well with Fe content in the sediment. Cyanobacteria was the dominant specie in the isolated bays during all periods. In common water period, algae biomass was positively correlated with pH and negatively correlated with water depth. Nutrient concentrations and algae cell density in the shallow dished lakes were much lower than those of the other water bodies. In flood period, algae biomass was positively correlated with total phosphorus concentration and turbidity while variance of water quality among different water bodies was relatively small. Cyanobacteria, especially Microcystis, became the dominant specie in all water bodies, while algae cell density and biomass in the shallow dished lakes were the lowest. In drought period, shallow dished lakes were isolated from the main water body of Poyang Lake with very poor water mobility, which may increase the risk of algae bloom. Algae biomass was positively correlated with total nitrogen, ammonia nitrogen and water conductivity. In both flood and drought periods with high temperature condition, dissolved microcystin concentration correlated well with Fe content in the sediment. This indicated that Fe may promote microcystin production and Fe enriched red soil erosion around Poyang Lake may exacerbate the risk of algae bloom. The present study can provide some guidance for water pollution control and aquatic environment risk warning of Poyang Lake.