Limnological studies have long focused on the nine largest plateau lakes and ecological assessment of lake eutrophication in Yunnan. However, comprehensive surveys of small and medium-sized lakes and their response to multiple stressors are largely absent. Here, we combined multi-proxy sediment analyses and documentary data, aiming to identify the long-term pattern of diatom community changes under the influence of climate change and anthropogenic disturbances, and to quantify their driving strengths. The results showed that Xihu Lake was in a pre-impact state with little ecological variability before the 1950s. Thereafter, expansion of land use increased the nutrient input and altered the lake hydrology, resulting in a significant shift of dominant diatoms from Cocconeis placentula to Fragilaria spp. From 1997,accelerating nutrient enrichment and hydrological changes led to the replacement of benthic diatoms by planktonic ones, resulting in a consistent loss of macrophytes and a decrease of ecological stability. Therefore, the types and strength of catchment development should be fully evaluated for effective protection of small and medium-sized alpine lakes in the context of global warming.