Human activities, global warming, frequent extreme weather events, and changes in atmospheric composition affect the solar radiation reaching the Earth’s surface, affect mass and heat transfer at the air–water interface, and induce oscillations in wind-driven internal waves. This leads to changes in the spatiotemporal characteristics of thermal stratification in lakes, altering lake circulation patterns and vertical mass transfer. However, thermal stratification structures are often overlooked. The intensification of lake thermal stratification due to warming may lead to increased release of bottom pollutants, spreading through the dynamic behavior of the thermocline to the epilimnion. Moreover, the increased heat storage is beneficial for the growth and development of certain phytoplankton, resulting in rapid transitions of the original steady state of lakes. Consequently, water quality deterioration, ecological degradation, and declining biodiversity may occur. Conventional surface water monitoring may not provide comprehensive, accurate, and timely assessments. Model simulations can better predict future thermal stratification behaviors, reducing financial burdens, providing more refined assessments, and thus preventing subsequent environmental issues.