Microcystis blooms and the subsequent release of hepatotoxic microcystins (MCs) pose a serious threat to the safety of water for human and livestock consumption, agriculture irrigation, and aquaculture worldwide. Microcystin-LR (MC-LR), the most toxic variant of MCs, has been widely detected in a variety of environments such as water, sediments, plants, and many aquatic organisms. Conventional solutions of water treatment are costly, requiring specific infrastructure, as well as specialized personnel and equipment. Therefore, these solutions are not feasible in many rural areas or in the treatment of large reservoirs. In this regard, low-cost and low-technology solutions, such as constructed wetlands (CWs), are attractive solutions to treat surface waters contaminated with toxic cyanobacteria blooms from lakes, ponds, reservoirs, and irrigation systems. In line with this, the main aim of this work was to evaluate the potential of CWs for the treatment of water contaminated with MC-LR produced by Microcystis aeruginosa-LEGE 91094. For that, microcosms (0.4 × 0.3 × 0.3 m) simulating CWs were assembled with Phragmites australis to treat lake water contaminated with Microcystis aeruginosa cells and MCs. Results showed removal percentages of M. aeruginosa cells above 94% and about 99% removal of MC-LR during 1 week treatment cycles. CWs maintained their functions, regardless the presence of MC-LR in the system, and also showed significant removal of nutrients (ammonium ion removal up to 86%) and organic matter (removal reaching 98%). The present work indicates that CWs have the potential for removal of cyanobacterial cells and cyanotoxins, which can be useful for the treatment of eutrophic waters and provide water of sufficient quality to be used, for instance, in agriculture.