Characterization of spatiotemporal variation of water quality is a basic environmental issue with implications for public health in China. Trends in the temporal and spatial distribution of water quality in the Huai River System (HRS) were analyzed using yearly surface water quality data collected from 1982 to 2009. Results showed that the water quality of the main stream deteriorated in the 1990s and early 2000s but has been ameliorated since 2005. The sections that were classified as severely polluted from the monitoring data were located largely in the middle reach. The water quality of HRS fluctuated during the period 1997-2009; it has improved and stabilized since 2005. In terms of spatialized frequency of serious pollution, heavily polluted regions were mostly concentrated in the area along several tributaries of the Ying, Guo and New Sui Rivers as well as the area north of Nansi Lake. These regions decreased from 1997 to 2009, especially after 2005. Our analysis indicated that water pollution in HRS had a close relation with population and primary industry during the period 1997-2009, and implied that spatiotemporal variation of surface water quality could provide a scientific foundation for human health risk assessment of the Huai River Basin.