Abstract: Lakes in the Inner Mongolia section of the Yellow River Basin play an irreplaceable role in regulating the climate and maintaining the ecological balance, etc. The water environment of the lakes is under threat due to the influence of natural and anthropogenic factors. In order to investigate the reasons for the high background value of total dissolved solids (TDS) in lakes in the Inner Mongolia section of the Yellow River Basin, and to comprehensively grasp the capacity of its water environment, the water quality parameters were analyzed based on the water quality monitoring data of 97 lakes in the Inner Mongolia section of the Yellow River Basin using principal component factor analysis (PCA/FA) and correlation analysis, and the water quality index (WQI) was used for the evaluation of water quality. The results showed that most of the water quality conditions of the lakes in the Inner Mongolia section of the Yellow River Basin were concentrated in the poor (39.2%) and moderate (47.4%) intervals, and only five lakes reached good water quality. TDS values were determined to be the key influence factor affecting the lakes by cluster analysis (CA). APCS-MLR and PMF models were used to quantitatively analyze the contribution of pollution sources to each water quality parameter. The fitting result R² indicated that the PMF model was more suitable for the allocation of pollution sources in the Inner Mongolia section of the Yellow River Basin, and the percentage of pollution sources was agricultural livestock and poultry breeding pollution (32.4%) > rural living pollution (26.9%) > agricultural cultivation pollution (23.9%) > industrial pollution (16.8%). This paper comprehensively evaluates the water environmental quality of lakes in the Inner Mongolia section of the Yellow River Basin and reveals its main influencing factors to provide scientific support for the high-quality protection and restoration of lakes in the Yellow River Basin.