Mesotrophic lakes and reservoirs, as critical sources of drinking water, have unclear mechanisms for the formation of its occasional algal blooms and the dynamics of nutrient limitations. This study took the Reservoir Duihekou in Zhejiang as a research object and revealed the fluctuation in algal growth rates and the dynamic coupling relationship between growth rates and nutrient quotas through four years of in situ monitoring. The results showed that during the diatom dominance phase (December to April, DIA), the in situ algal growth rate (μ) fluctuated significantly, ranging from -1.10 to 2.76 d_^-1, while during the cyanobacteria dominance phase (July to August, CYA), the range is -0.43 to 0.81 d_^-1, higher than in eutrophic waters, indicating the rapid proliferation potential of algae in mesotrophic systems. Algal growth rates during DIA were mainly dominated by nitrogen cell quotas (CQ_N, P<0.001). This might be attributed to the inhibitory effects of light limitation and low temperatures on chlorophyll synthesis and nitrogen assimilation efficiency. Consequently, if the gradual increase in temperature and light intensity during spring coincided with an elevated nitrogen cell quota in algae, it could potentially trigger a diatom bloom. While the growth rates during CYA were synergistically regulated by phosphorus cell quotas (CQ_P) and phosphorus environment quotas (EQ_P, P<0.001). It suggested maintaining total phosphorus (TP) below 22 μg/L (95% CI: 15–32 μg/L) could effectively control cyanobacteria blooms (Chl.a >10 μg/L). This study innovatively introduced dynamic cellular quotas to analyze algal growth mechanisms, resolving traditional reliance on relationships between environmental nutrient concentrations and algal biomass or nitrogen-to-phosphorus ratios to judge the nutrient limitation types. This provides a new theoretical framework for water quality management and bloom warning in mesotrophic lakes and reservoirs.