Water quality is a key indicator of human health. Wuliangsuhai Lake plays an important role in maintaining the ecological balance of the region, protecting the local species diversity and maintaining agricultural development. However, it is also facing a greater risk of water quality deterioration. The 24 water quality factors that this study focused on were analyzed in water samples collected during the irrigation period and non-irrigation period from 19 different sites in Wuliangsuhai Lake, Inner Mongolia, China. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were conducted to evaluate complex water quality data and to explore the sources of pollution. The results showed that, during the irrigation period, sites in the middle part of the lake (clusters 1 and 3) had higher pollution levels due to receiving most of the agricultural and some industrial wastewater from the Hetao irrigation area. During the non-irrigation period, the distribution of the comprehensive pollution index was the opposite of that seen during the irrigation period, and the degree of pollutant index was reduced significantly. Thus, run-off from the Hetao irrigation area is likely to be the main source of pollution.