Determining the spatiotemporal water quality patterns and their corresponding driving factors is crucial for lake water quality managements. This study analyzed hydrological data and concentrations of 11 water quality parameters, including total nitrogen, total phosphorus, ammonia nitrogen and chlorophyll–a (Chl–a), for water samples collected from 15 sampling sites between 2009 and 2014. The water quality of sites in the northern Poyang Lake–Yangtze River waterway was influenced by different environmental parameters compared to sites in central lake, especially for Chl–a concentration. All pollutant parameters were significantly higher in the river phase (water level 14 m) (p < 0.05). These results were confirmed via principal component analysis, which identified three principal components that explained over 79% of the dataset variance. Among all the parameters related to climatic factors, eutrophication and organic pollution were the most important contributors in water quality. Dilution was the controlling factor that drove the seasonal variability in the water quality of the Poyang Lake, China. This work further indicated that regulating pollutant effluents in tributaries and water level within the lake could improve the water quality in Poyang Lake, which may give some impetus for water quality management.