In the context of a warming climate, there is increasing evidence that lake ecosystems in remote alpine areas far from human activities have undergone significant changes. However, the complex interplay of climatic, non-climatic factors, and watershed processes complicates the understanding of lake ecosystem responses to global changes in alpine areas. In this study, we chose Lake Julong, an alpine lake in Weixi, Yunnan Province, as the research site, and analyzed the history of lake basin ecosystem changes over the past two centuries using grain size, magnetic susceptibility, elements, and diatoms in the sedimentary record, in conjunction with climatic records and remote sensing data. The results showed that the regional temperature increased during 1970-1996, the glaciers covering the Lake Julong watershed ablated in a large area, and the geochemical indicators (total organic carbon, total nitrogen, median particle size, sedimentation rate) indicated the enhancement of lake hydrodynamics and a reduction in nutrient loads. After 2000, regional precipitation decreased, and temperature continued to increase, leading to the disappearance of permanent glaciers in the watershed and an increase in bare land area. Elemental and magnetization indexes indicated enhanced weathering and erosion of soils. The diatom community of Lake Julong was dominated by Staurosira construens and Staurosirella pinnataduring the study period. During the period of enhanced hydrodynamics, the relative abundance of Nitzschia fonticolaa nd epiphytic Achnanthidium minutissima increased. The primary composition of diatoms (expressed as PCA Axis 1 scores) reached a tipping point in the 1960s and then remained relatively stable, in contrast to the continuous changes in climatic, hydrological, and erosional indicators. However, the secondary composition of diatom communities continued to change after the 1960s, indicating that processes such as watershed climate, hydrology, and erosion had begun to affect rare species in the diatom community. This suggests that the entire diatom community may be increasingly affected under future global change. This study highlights the combined effects of hydrology, erosion, and glacier retreat on aquatic communities in alpine lakes under climate change, clarifying the nonlinear response characteristics of these communities to global changes.