Arsenic (As) metabolism in freshwater algae at different growth phases has rarely been documented. To address this gap, this study was conducted to assess the intra- and extracellular As metabolism, along with speciation changes, in Microcystis aeruginosa across three growth phases. The treatment involved varying concentrations of As (0, 0.4, 0.6, 0.8 and 1 mg/L, in the form of arsenate, iAsV) under three phosphorus levels (0.02 mg/L as low, 0.1 mg/L as medium, and 0.5 mg/L as high P in the form of phosphate). The findings revealed that extracellular iAsV remained the dominant As species during the lag and exponential growth phases of M. aeruginosa in the growth media, while intracellular trivalent As (iAsIII) emerged as the pronounced species during the exponential growth phase, but also exhibited a significant negative correlation with the P levels. Moreover, elevated P levels had promoted the formation of intra- and extracellular dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA) in the exponential growth phase. During the stationary growth phase, intracellular iAsV was found to decrease with the increasing P levels. During the whole growth phases, P had consistently reduced algal As absorption levels. The significant promotion of algal As absorption in response to iAsV was observed only during the lag growth phase. The As bioaccumulation exhibited a correlational relationship with the algal reproduction. Both low and high P levels (0.02 and 0.5 mg/L) decreased the accumulation of As in algae cells during the exponential and stationary growth phases. The transformation and release rate of As were concomitantly influenced by P, and exhibited the same trends within the growth phase. These trends differed between the exponential and stationary growth phases, with an inhibitory effect being present during the former, while a promotional effect was observed during the latter. This study provides insight into potential As hazards in freshwater lakes with algae bloom.