High-altitude areas are less directly disturbed by human activities, and regional warming and atmospheric deposition have become important factors in affecting the environment and ecological health of alpine lakes. With an increasing number of alpine lakes in China experiencing persistent ecological changes, a comparative analysis of different types of lakes and bioindicators is needed for systematically identifying ecological risks of alpine lakes. In this study, six alpine lakes in Northwest Yunnan were selected to reconstruct the history of changes in lake environment and algae over the past 150 years through multi-indicator analyses of sediment grain size, total nitrogen (TN) content, nitrogen stable isotopes, and algae (pigments and diatoms) and by combining with historical data, focusing on identifying similarities and differences in the patterns of algal abundance and diatom communities responding to regional environmental changes along the altitudinal and water-depth gradients, as well as the lakes' Difference. Among the deep-water lakes (Dinggongniang , Gaigong Cuona, Wodi Co), Dinggongniang Co maintained stable algal pigment concentrations, while Gaigong Cuona and Wodi Co displayed increasing primary productivity. In the shallow lakes (Shudu, Dinggong shallow zone, Bigu Tianchi), productivity rose gradually in Shudu, but chlorophyll levels declined in Dinggongniang and Bigu Tianchi. Variance decomposition analysis showed that the driving strength of warming effect on sediment pigment content was generally greater than that of atmospheric deposition (total nitrogen content), while there exists obvious lake differences in diatom community and algal production under the water depth gradient. Specifically, the diatom communities in deep-water lakes (Dinggongniang Co, Gaigong Cuona, Wodi Co) were dominated by small planktonic species, and the shallow-water lakes (Dinggong Co, Shudu Lake, Bigu Tianchi) were dominated by benthic species. The diatom community in Dinggongniang Co has undergone a significant shift since 1930, mainly characterized by a rapid rise in small planktonic species (Pantocsekiella comensis). In contrast, Gaigong Cuona and Wodi Co remained stable, whereas shallow lakes showed multiple community transitions. Unlike the deep-water lakes, the diatom communities of the three shallow-water lakes showed significant or multiple changes. Comparative analysis of the lakes showed that algal productivity and diatom community structure in alpine lakes generally showed a more consistent trend of over time. In conclusion, algal changes in alpine lakes under the combined influence of climate warming and atmospheric deposition showed a heterogeneous regional pattern, and more sensitive response can be found in sites from lower elevation and shallow lakes.