Alpine lakes are often located remotely without the direct impacts of human activities, and usually characterized by small size, low nutrient level, and simple trophic structure, and thus being highly sensitive to climate change and nutrient inputs. Along the southeastern margin of Qinghai-Tibet Plateau, there exists a high flux in nitrogen deposition and a significant increase in temperature. Previous studies had shown that there might exist regional heterogeneity in lake responses in this area that can be linked with lake types and landscape features. In this study, three small-sized lakes (Gaigong Cuona, Wodi Co and Bigu Tianchi) with different water depths, all of which are slightly alkaline and located below the tree line, were selected for sediment surveys and comparative analyses. Multi-proxy analyses, including sample dating, physio-chemical and algal indicators (e.g., diatom assemblage and algal pigments), were carried out in combination with data collation on quantitative reconstruction of regional climate and nitrogen deposition, aiming to evaluate the degree of concordance in algal changes over the last three centuries and the mediating effect of lake depth among lakes. The results showed that there were significant differences in the dominant diatom species and composition of diatom community across lakes. The diatom community was dominated by plankton species (~ 82%) in Gaigong Cuona (maximum depth=39.4 m), including Pantocsekiella ocellata and P. comensis. In Wodi Co (maximum depth=20.7 m), planktonic and benthic taxa accounted for about 50% of the community, respectively, and the dominant species were Pantocsekiella ocellata and Staurosira construens. In contrast, benthic diatoms (~ 99%) was highly dominant in the shallowest lake of Bigu Tianchi (maximum depth=1.7 m), including Achnanthidium minutissimum and Encyonopsis microcephala. In both deep-water lakes (Gaigong Cuona and Wodi Co), the diatom composition showed no significant shift but the primary production (i.e., pigments) displayed a continous increase over the past 300 years. Meanwhile, the diatom community in the shallow lake (Bigu Tianchi) showed obvious changes while the pigment concentration showed a general trend of declining. Specifically, the relative abundance of Achnanthidium minutissimum increased and became the dominant species since ~1968. It was further shown that environmental factors may differ strongly in driving diatom assemblages across lakes. The diatom community was mainly affected by hydrological fluctuations in Gaigong Cuona, but was mainly related to total nitrogen (TN) in both Wodi Co and Bigu Tianchi. Along the depth gradient, TN had a stronger effect on diatom community in shallower lakes. Regarding the driving factors of lake primary production, the hydrological and temperature changes were significant in Gaigong Cuona, TN and temperature factors were obvious in Wodi Co, and the hydrological and TN fluctuations were important in Bigu Tianchi. In conclusion, the algae succession in alpine lakes was found to be significantly linked with lake typology such as water depth, and there may exist a higher degree of sensitivity in algal changes in shallow-water lakes in response to regional warming and atmospheric deposition in Southeast Tibet Plateau.