In the present study, the water quality of 13 lakes, which are located in Yunnmi-Guizhou Plateau and total areas are more than 10km², was evaluated according to the data from the investigation in 2008. TTie variation of trophic state was analyzed by comparing to historical data prior to 1988-1992. Furthermore, principle component analysis (PGA) was also used to evaluate the effect of water quality parameters, in which the comprehensive evaluation scores erf the 13 lakes were calculated according to extracted six principle components of the PCA. Changes in water quality of all lakes, except Lake Chenghai, was able to be explained by influences of trophic state, organic pollution and agricultural non-point source pollution under increasing anthropogenic pressure. However, water quality of Lake Chenghai was mainly affected by changes in water salinity. In addition, we also proposed the comments and suggestions about protection and management of these lakes.