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• Low nitrogen availability promotes the downward transport of Microcystis biomass. • The increased downward transport of biomass is driven by physiological processes. • Carbohydrate accumulation is mainly due to a downregulation of glycolysis. • The increased downward transport of biomass accelerates the dissipation of bloom. Nitrogen availability is one of the key factors affecting the dynamics of non-diazotrophic cyanobacterial blooms in eutrophic lakes. While previous studies mainly focused on the promoting effect of nitrogen on the growth of cyanobacteria, this study aimed to investigate the role of nitrogen availability in the downward transport of biomass and its effects on the dynamics of Microcystis blooms. We performed field enclosure experiments which demonstrated that nitrogen availability negatively affects the downward transport of biomass. With a nitrogen loading of 0.02 g N m−2 d−1, the Microcystis biomass in the water column decreased by 56.2% over a 4-day period. During the same period of time, the average sinking ratio was 0.23 d−1; moreover, the termination of biomass growth was detected. At the notably higher nitrogen loading of 0.5 g N m−2d−1, the downward transport of biomass could still compensate for the biomass growth, although the average sinking ratio was lower at 0.16 d−1. Additional laboratory culture experiments demonstrated that the increase in the downward transport of Microcystis occurred in parallel to an increase in the carbohydrate content and a decrease in gas vesicle content. Further proteomic analysis indicated that the carbohydrate accumulation induced by nitrogen deficiency was a result of the slowing down of catabolic consumption, especially the downregulation of glycolysis. Thus, our study suggests that increased intracellular carbohydrate accumulation at low nitrogen availability causes a higher sinking ratio of Microcystis , indicating that nitrogen limits the duration of Microcystis blooms; thus, decreased nitrogen availability may lead to increased sinking of biomass out of the water column, accelerating the dissipation of Microcystis blooms. [ABSTRACT FROM AUTHOR]