Climate change-induced extreme weather events, including prolonged droughts and intense rainfall, exert a significant influence on river inflows. These inflows act as vital conduits for nutrient transport, water quality modulation, and the regulation of thermal dynamics in lakes and oceans. In this context, this study conducts a comprehensive examination of the multifaceted effects stemming from river water characteristics, snowmelt water influence, and shifts in precipitation patterns on the stratification dynamics of Lake Biwa in Japan. To facilitate these investigations, a hydrodynamic model was developed to simulate thermal stratification in Lake Biwa. The results demonstrate that an increase in precipitation and river water flow, specifically doubling these factors, leads to noticeable cooling of the lake’s surface layer and a consequent destabilization of stratification during the stratification period. Conversely, halving these factors stabilizes stratification. Furthermore, elevating river water temperature by 5 °C raises water temperature near the upper thermocline, encouraging vertical mixing within the surface layer. Conversely, a 5 °C decrease induces significant temperature fluctuations and an unstable stratification extending from the surface to deeper layers. Notably, the spatial variance in water temperature within Lake Biwa is profoundly influenced by fluctuations in river water temperature. This study underscores the critical importance of considering river plumes in the study of material circulation, stratification dynamics, and ecological well-being in lakes and oceans. Given the mounting concerns related to eutrophication and the prevalence of anoxia in aquatic ecosystems, this research provides invaluable insights into assessing the impacts of river plumes on Lake Biwa’s stratification structure and seasonal dynamics.