To identify the water quality variation of typical lakes in Inner Mongolia, the water quality data of Lake Wuliangsuhai, Lake Daihai and Lake Nanhai from 2013 to 2023 were obtained. The comprehensive pollution index and trophic level index were employed to analyze the evolution characteristics and trends of water quality in each lake. Pearson correlation analysis was applied to investigate the correlation between water quality indicators and these two indices in these three lakes. The temporal trend of the nitrogen to phosphorus molar ratio was analyzed, aiming to explore the main factors affecting the lake water quality. The results indicated that during 2013-2023, chemical oxygen demand (COD_Cr ), total phosphorus (TP), ammonia nitrogen (NH₃ -N), and chlorophyll- a(Chl .a ) in Lake Wuliangsuhai, Lake Daihai, and Lake Nanhai exhibited a declining trend. However, TN in Lake Daihai reached its peak value in 2020, and remained at the water standard of inferior Class V. The eutrophication level of Lake Wuliangsuhai showed a trend from severe to moderate and then to mild. With the testing project of “diverting water from the Yellow River into Daihai”, the eutrophication of Lake Nanhai had changed from severe to moderate. Lake Nanhai, serving as a tourist attraction, has been in a state of severe eutrophication for many years. The comprehensive pollution index indicated that the water quality of Lake Wuliangsuhai was improving. Under environmental remediation, the deteriorated water quality of Lake Daihai and Lake Nanhai was gradually improving, but the remediation measures could be further strengthened. Among them, Lake Daihai and Lake Nanhai were significantly polluted by nitrogen, and the reduction of TN, TP, and COD_Cr should become the priority task for these three lakes. Regression linear model analysis showed that Chl .a in these three lakes was positively correlated with TN and TP concentrations respectively. The ratio of nitrogen to phosphorus revealed that phytoplankton growth was favorable in the lake during most periods. Phosphorus may be the main influencing factor of Chl .a in Lake Wuliangsuhai, while Lake Daihai and Lake Nanhai may be limited by both nitrogen and phosphorus.