Water scarcity is perceived as a global systemic risk since there is an inexorable rise in water demand. An ecological engineering system mimics a natural ecosystem by balancing the trophic conditions for effective treatment of wastewater in a sequential manner. The present study was designed using emergent, floating and submerged macrophytic plants in a systematic approach. The study was evaluated with several components such as plants (water hyacinth, water lettuce and water thymes), aeration (supply of oxygen), and physical adsorption (activated carbon). Domestic wastewater collected from the local effluent treatment plant was treated individually and by combining all the components. Diverse experimental setups viz., lake sediment (control reactor), aeration, activated carbon blocks, water hyacinth, water lettuce, and water thymes were individually studied. Further the above components were combined, such as lake sediment + aeration + activated carbon blocks with plants like water hyacinth, water lettuce, and water thymes. The study inferred along with phytoremediation, and the external factors enhanced the treatment performances. Water hyacinth documented enhanced chemical oxygen demand removal efficiency of 85.71%, followed by water lettuce (80%), and water thymes (77.14%) along with the plants, both aeration, and activated carbon had stimulated the wastewater treatment. The highest removal efficiency of nitrate (70.23%), phosphate (63.64%), and sulphate (61.16%) were observed in water hyacinth due to its thick roots, and fibrous tissues reported effective treatment. The study hypothesized that these processes could be an effective strategy to restore the lakes and regulate the environmental flow. The study infers that an ecological engineering system symbiotically enables to self-organize the ecosystem within the boundary. © 2021 Elsevier Ltd