Microcystins are cyanotoxins that can be produced by cyanobacteria species such as Microcystis aeruginosa. Due to the presence of microcystins in water bodies and aquatic organisms, it needs to be monitored. Furthermore, additional studies are required in the implementation of alternative and sustainable water treatment methods. The aim of this study was to investigate the potential of Myriophyllum aquaticum to prevent the harmful effects induced by M. aeruginosa aqueous extract in Rhamdia. quelen usingbiomarkers and to assess whether the plant can be suitable for phytoremediation in aquatic ecosystems. In the first experiment, R. quelen was exposed to 1 and 10 μg.L–1 of microcystins through an aqueous extract dissolved in the bioassay’s water. Second, tanks containing the same test concentrations of microcystins were treated by phytoremediation using M. aquaticum at 10 g.L–1, for 7 days. After that, treated water was used in a new bioassay with fish exposure. The results showed that phytoremediation decreased the microcystin concentration in water, and different biomarker analyses demonstrated that M. aquaticum treatment prevented DNA damage, hematological alterations, and tissue damage in R. quelen. The phytoremediation with M. aquaticum can be a sustainable and cost-effective alternative to water treatment, highlighting its role in enhancing water quality and supporting biodiversity conservation. These results support the importance of adopting more restrictive legal limits for cyanotoxins in water to protect native aquatic species and promote sustainable water resource management.