Microcystins (MCs) are cyanotoxins produced by different genera of cyanobacteria in aquatic environments. It’s a cyclic heptapeptide and toxic to many organisms. Over 90 MCs variants are described, with the –LR (MC-LR) one of the most toxic. In the Jacarepagua lagoon (RJ), cyanobacteria are abundant and reported since 1996 producing MCs. The dynamics of this molecule in the aquatic environment consists to bioaccumulate in organisms, adsorption to sediment particles and biodegradation. This study aimed to evaluate the influence of some factors such pH, atmosferic temperature and aeration, on the dynamics in the compartiments of Jacarepagua Lagoon, In addition, we evaluated the biodegradation of MC by microbial assemblages of water and sediment, characterizing them as to their bacterial composition by metagenomics. Experiments with duration of 7 days were conducted to assess both the adsorption and biodegradation activity. The parameters analyzed were not able to cause the return of preexisting toxins in the sediment to the water. Adsorption was also evaluated upon addition of a known concentration of the toxin. Acidify conditions caused an immediate reduction of the same in the water column, possibly attributed to the adsorption. Heating at 45 °C leads to reduction in the total of the toxin into the water over the 7 days, which did not occur at 25 ° C. Aeration in the water / sediment interface caused a intense decrease in the fourth day, and overall throughout the 7 days, which was not without aeration. Then, the effects evaluated may increase the adsorption capacity of the MC to sediment. However, sediment treatment with sodium azide (antimicrobial) and sterile water showed that even after handling procedures was able to degrade the toxin and thus this process has occurred simultaneously for adsorption. In biodegradation experiments by microbial assemblage (0,45 µm diameter) of water and sediment, MC was eliminated over 7 days. Microbial assemblages <0,22 µm (nanobacteria) were also evidenced and able to biodegrade the MC-LR. The characterization of water and sediment bacterial community by metagenomics showed different compositions between these compartments. Phylum Actinobacteria and Proteobacteria as were the most abundant in water, unlike interstitial water where the candidate division OP3 was the most abundant. In the raw sediment, which covers a more general community, the predominant were Chloroflexi, Proteobacteria and Firmicutes. Furthermore, it was observed of many genera described in the literature capable of biodegrading MC-LR, suggesting possible participants in the biodegradation process in the compartments of the Jacarepagua lagoon, which does not invalidate the participation of other microorganisms in general through a shared activity.