The aquaculture industry in Brazil has grown immensely resulting in the production of inefficiently discarded wastewater, which causes adverse effects on the aquatic ecosystem. The efficient treatment of aquaculture wastewater is vital in reaching a sustainable and ecological way of fish farming. Bioremediation in the form of the Green Liver System employing macrophytes was considered as wastewater treatment for a tilapia farm, COOPVALE, in Itacuruba, Brazil, based on previously demonstrated success. A large-scale system was constructed, and the macrophytes Azolla caroliniana, Egeria densa, Myriophyllum aquaticum, and Eichhornia crassipes were selected for phytoremediation. As cyanobacterial blooms persisted in the eutrophic wastewater, two microcystin congeners (MC-LR and -RR) were used as indicator contaminants for system efficiency and monitored by liquid-chromatography–tandem-mass-spectrometry. Two trial studies were conducted to decide on the final macrophyte selection and layout of the Green Liver System. In the first trial, 58% MC-LR and 66% MC-RR were removed and up to 32% MC-LR and 100% MC-RR were removed in the second trial. Additional risks that were overcome included animals grazing on the macrophytes and tilapia were spilling over from the hatchery. The implementation of the Green Liver System significantly contributed to the bioremediation of contaminants from the fish farm.