Phytoremediation offers a sustainable solution to aquaculture pollution, but studies with critical evaluations of the treatment performances of macrophyte systems are limited. This study intended to evaluate the roles and treatment profiles of Spirodela polyrhiza (L.) Schleid. and Lemna sp. systems in terms of ammonia, nitrate, nitrite, phosphate (NH3-N, NO3 --N, NO2 --N, PO4 3-), chemical oxygen demand (COD), turbidity, and total suspended solids (TSS) on fish farm wastewater and to elucidate the rationale behind the removal of the pollutants and the changes in a raceway pond rig. The nitrogen and phosphorus removal in the Spirodela polyrhiza monoculture system outperformed the other configured systems. An 81% reduction in ammonia (to 3.90 mg of NH3-N/L), and sharp declines of up to 75%, 88%, and 71% in TSS, turbidity, and COD levels were recorded within two days, while significant decreases in nitrate, nitrite, and phosphate levels were observed. This indicated that the system could inhibit nitrate and nitrite spikes in waters (nitrification) via reducing the available ammonia and limiting subsequent nitrite and nitrate conversion, while reducing TSS in algal-bloom wastewater via shading. High biomass productivity and superior protein content were observed in the macrophyte systems (S. polyrhiza + Lemna sp. polyculture system), with up to 112% and 12% increases, respectively. This study demonstrated that the S. polyrhiza monoculture system is effective at treating fish farm wastewater, lowering the levels of relevant inorganic and organic pollutants, and it could be used as a biofilter for natural waters, preserving the existing ecology.