<p>Impacts on the ecological health of the numerous reservoirs located in the Lancang River Basin (LRB), China has drawn significant attention in recent years. Previous studies here mainly dealt with the conveyance and interception of nutrients by these reservoirs. This study focuses on the influences of hydrological processes in these reservoirs on water chemistry and the implications for host ecosystems. Longitudinal variations of water temperature, water chemistry, and H and O isotope values in the main stem of the Lancang River, and vertical variations in the reservoirs, were analyzed in relation to water sources and mixing. Results indicate that the main stem river waters enter the middle/bottom layers of the reservoirs through interflow/underflow in warm/cold seasons, and that waters from the tributaries enter the surface of the reservoirs through overflow. The large reservoirs are permanently stratified, which is verified by variations of δ¹⁸O values versus Cl⁻ concentrations. Consequently, surface waters cannot be fully renewed, and phosphorus derived mainly from tributary inflows tends to accumulate in surface layers. These conditions facilitate the development of algal blooms. The mechanism proposed here explains the progressive increases in algal densities observed in the large reservoirs. This study suggests that coupling of permanent stratification and distinctive circulation patterns substantially raises the risk of the development of algal blooms in these large reservoirs. Therefore, long-term and comprehensive observations focused on thermal stratification, water circulation, nutrient cycling, and phytoplankton growth are an urgent task in the future.</p>