In Egypt, most fish farms use water of agricultural drainage originated from agricultural activities that may contaminate farmed fish. This work was conducted to assess a novel wastewater treatment using combined protozooplankton with magnetic-EDTA@chitosan nanocomposite (ME@CS NC), to dwell with high concentrations of heavy metals and ammonia. A highly significant reduction (p < 0.01) was observed in the concentrations of Pb, Mn, Al and Cd on applying the treatment. The estimated decrease percentages were 99.9, 99.6, 98.8 and 93.3, respectively, whereas Ni showed a reduction of 90.3%. Simultaneously, ammonia in wastewater was significantly reduced (p < /em><0.01). Water environmental parameters of EC, pH, TDS, and NO₂ were reduced by 2.4, 3.7, 7.4, and 43.3%, respectively, while PO₄, and NH₃ were reduced by 76.7 and 94.4%, respectively. Moreover, COD, nitrite, nitrate and phosphate physicochemical parameters were significantly reduced (p < /em><0.05), by 41.4, 54.9, 63.3, 64.4%, respectively. Hence, the combined treatment of ME@CS nano-composite and protozooplankton is recommended to be implemented in semi-intensive and modern intensive aquaculture systems to manage less water consumption and attain healthy fish for human consumption.