Based on the monitoring data of 78 monitoring stations from 2003 to 2012, five key water quality indexes (biochemical oxygen demand: BOD5, permanganate index: CODMn, dissolved oxygen: DO, ammonium nitrogen: NH3-N, and total phosphorus: TP) were selected to analyze their temporal and spatial characteristics in the highly disturbed Huaihe River Basin via Mann-Kendall trend analysis and boxplot analysis. The temporal and spatial variations of water pollutant concentrations in the Huaihe River Basin were investigated and analyzed to provide a scientific basis for water pollution control, water environment protection, and ecological restoration. The results indicated that the Yinghe River, Quanhe River, Honghe River, Guohe River, and Baohe River were the most seriously polluted rivers, followed by Hongze Lake, Luoma Lake, Yishuhe River, and Nansi Lake. BOD5, CODMn, and NH3-N were the major pollution indexes, for which the monitoring stations reported that more than 40 % of the water quality concentrations exceeded the class IV level. There were 21, 50, 36, and 21 monitoring stations that recorded significantly decreasing trends for BOD5, CODMn, NH3-N, and TP, respectively, and 39 monitoring stations showed a significantly increasing trend for DO. Moreover, the water quality concentrations had a certain concentricity and volatility according to boxplot analysis for the 20 monitoring stations. The majority of monitoring stations recorded a large fluctuation for the monitoring indexes in 2003 and 2004, which indicated that the water quality concentrations were unstable. According to the seasonal variations of the water quality concentrations in the mainstream of Huaihe River, the monthly variation trends of the BOD5, CODMn, DO, NH3-N, and TP concentrations were basically consistent among the seven monitoring stations. The BOD5, CODMn, NH3 -N, and TP concentrations were affected by the change of the stream discharge; changes in DO and NH3-N concentrations were influenced by the regional environmental temperature, and the DO and NH3-N concentrations decreased when the water temperature increased.