Sixty-seven water sampling sites in the Yili-Taoge plain river networks of the upstream area of the Taihu Basin were set to characterize its water quality with spatiotemporal distribution. Water sampling trips were conducted in January (winter), April (spring), August (summer), November (autumn) of 2014, and main water quality parameters were concentrated on nutrients and organic matters. Spatial and seasonal variations of water quality were analyzed by using the multivariate statistical methods and water quality were assessed by employing the comprehensive water quality identification index. The results indicated that pollution degree in the research area was severe. The averaged concentrations of total nitrogen (TN), total phosphorus (TP) and permanganate index (COD_Mn) were 4.93 mg/L, 0.26 mg/L and 7.63 mg/L, respectively. One-way multivariate analysis and cluster analysis showed significantly spatiotemporal patterns of pollutants. Pollution levels in winter and spring were higher than that in summer and autumn. Pollution of nitrogen and phosphorus were heavier in the Wuxi and Changzhou areas, whereas organic matter pollution was more serious in the Yixing and Liyang areas. Water quality in the upstream plain river networks can meet the criteria of Grade IV or V of National Standards for Surface Water Quality, characterized by pollution of TN, TP and COD_Mn.