Poyang Lake Migratory Bird Sanctuary includes Bang Lake, Sha Lake, Dahu Lake, and estuaries of the Xiu and Gan Rivers in the Migratory Bird Natural Reserve. Water samples were collected and analyzed to study spatial and temporal water quality variation. Strong seasonal variation of water quality was found. The water quality of Bang Lake was relatively poor compared to Sha and Dahu Lakes in the wet season, but better in the normal season. During the dry season, the water quality of Bang Lake is negatively affected by the activity of migratory birds. According to the correlation analysis of monthly concentrations of each parameter, the concentrations of COD, NH4 +–N, and NO3 −–N were highly correlated. The correlation index was 0.829 and significance index was 0.042 < 0.05. From north to south within Bang Lake, the concentration of TN decreased; however, the concentration of Chl-a increased. From east to west within Bang Lake, concentrations of COD, NH4 +–N, NO3 −–N, and Chl-a increased. The Xiu and Gan Rivers influence the water quality of Bang Lake, especially in the northeast area of the lake. The water quality of Bang Lake only reached Chinese water quality standard level IV or V according to a fuzzy comprehensive evaluation. The evaluation factors impacting Bang Lake are TN>TP>NH4 +–N>COD, in order of decreasing importance. The waters of Poyang Lake Migratory Bird Sanctuary have been polluted; one of the important contributing factors was migratory birds’ disturbance and feces. © 2015, Science Press, Institute of Geochemistry, CAS and Springer-Verlag Berlin Heidelberg.