Large scale phosphate mining in the Huangbaihe River Basin, China has reduced the self-purification capacity of the basin's fresh water. Three years (2014)(2015)(2016) of monitoring data and chemometric analysis were used to identify the dominant pollutants and define their spatial distribution in the basin. Principal component analysis was applied to determine the contribution of the individual pollutants. Total phosphorus (TP) 53%, water temperature (TEMP) 27%, and total nitrogen (TN) 20% proved to be the dominant problems. A discriminant functions (DF) model was developed to classify the study area into high, moderate, and low pollution zones. The DF coefficients were applied to analyze the correlation between DF and the measured parameters and it was found that TP, TN, and TEMP were positively correlated with the DF, indicating that these parameters were the most important. Finally, the results were compared with the locations of the mining activities, which revealed that TP is higher in the upper sub-basins, Xuanmiaoguan and Tianfumiao, where most of the high pollution zones are located and more than 78% of the areas are affected by the phosphate mines. It is concluded that the phosphate mining is the major source of pollution and TP is the dominant pollutant responsible for the total water quality variation in the river basin. More effective management measures have to be taken to reduce phosphorus runoff into the reservoir watersheds.