Algae are crucial primary producers in lake ecosystems, and their biomass and community structure can reflect water pollution and ecological status. As an important component of algae, the species composition characteristics of diatoms are also sensitive indicators for evaluating lake environmental quality. However, there is still a lack of systematic analysis regarding whether there are significant differences in the variation patterns and response mechanisms of algal biomass and diatom communities in lakes with different pollution levels. This study conducted seasonal investigations and comparative analyses in Lake Datun and Lake Yangzong, which have relatively high arsenic (As) pollution levels, and Lake Yilong, which is not affected by arsenic pollution, in Yunnan Province. The aim was to identify the main characteristics, driving factors, and key processes of algal changes 〖JP2〗under different arsenic pollution levels. Among the 55 surface water samples collected in this study, the concentration of water chlorophyll-a (Chl.a), which indicates algal biomass, was the highest in the eutrophic Lake Datun. Diatom compositions differed among the lakes and showed obvious seasonal fluctuations. Correlation analysis revealed a significant positive correlation between arsenic and Chl.aconcentrations in the lakes. This outcome indicates that phytoplankton are sensitive to arsenic stress in these lakes, and that the low arsenic levels exert a notable stimulating effect on algal growth. Meanwhile, arsenic was also significantly correlated with the main direction of diatom community changes. The results of variance decomposition analysis on algal data and environmental factors from the three lakes showed that the driving effect of the main environmental gradients on the succession of diatom community structure (PC1 index) was more significant than the fluctuation of Chl.a concentration (with average explained variances of 64.1% and 39.8%, respectively). The study results also revealed that the seasonal variation of water arsenic pollution is closely related to water temperature and lake depth type: increased water temperature promotes the chemical activity of arsenic and increases water arsenic concentration in shallow lakes, while in deep lakes, it limits the diffusion of sediment arsenic and the vertical migration of water arsenic through thermal stratification. In conclusion, the interactions between arsenic and factors such as water temperature, nutrients, and water depth under different pollution levels are significant, exerting important influences on the seasonal changes of algae and leading to large differences in the response intensities of different algal indicators. Therefore, for effective ecological assessment and restoration of lake arsenic pollution, it is necessary to comprehensively consider the combined effects of temperature and nutrient levels and conduct comparative analyses using multiple indicators such as algal biomass and diatom communities.