The plateau lakes of Yunnan are important both ecologically and economically in China. Nevertheless, the human impact on water quality in these lakes has become increasingly highlighted. The water quality of 10 plateau lakes was monitored regularly over the period of 2000 through 2004 for 24 parameters. Multivariate statistical techniques, including cluster analysis (CA), factor analysis (FA), and principal component analysis (PCA), were employed to better interpret information about the water quality and its pollution sources. No obvious data reduction from CA/FA was found because three principal components (PCs) needed 14 variables to explain 85.01% of the total variance. However, three latent factors accounted for pollution mainly from the following sources: agricultural activities, residential activities and anthropogenic-toxic pollution from industrial effluents, or other special activities. Box-whiskers plots were employed to visually interpret the spatiotemporal variations of water quality variables, which were highly correlated with three PCs. Three types of water quality (i.e., low-, medium-, and high-polluted lakes) were determined through CA based on the similarity of water quality variables. Our results may provide helpful information for the authorities to effectively manage the water quality and make sound policies.