Atmospheric deposition and climate change are altering alpine lake ecosystems at an accelerating rate. Biotic responses to the interactions of multiple stressors are underexplored in alpine lakes. This study explored diatom responses to climate change and nutrient supply based on multi-proxy sedimentary records in Erye and Sanye Lakes of the Taibai Mountain at the boundary between the subtropical and temperate climate zones of eastern China. Diatom communities of the two lakes shifted from large-sized benthic taxa to small fragilarioid species at the beginning of the 21st century, synchronous with an increase in diatom accumulation rate. Redundancy analyses showed that diatom communities were significantly correlated with catchment processes and nutrient inputs in both lakes, as well as climate warming in the upstream lake. Partial least squares path modelling revealed that catchment processes were more important than direct effects of climate warming and nutrient supply for explaining the observed shifts in diatom flora in the two alpine lakes. The comparison with diatom records in similar alpine lakes in the East Asian monsoon region reveals that responses of alpine lake ecosystems to warming and atmospheric deposition vary with different catchment settings and lake morphometry. Given that these alpine lakes serve as important water sources, recent biotic reorganization suggests that the protection of headwater systems should be given high priority, especially in rapidly developing and densely-populated regions.