The rapid population growth and uncontrolled pollutant discharge through various point and non-point sources have endangered the water body of Trimohoni, Dhaka. The water restoration here is necessary to support economic activity, sustainability, and ecological balance. The industrial and domestic waste mixed with Trimohoni’s water has caused eutrophication, resulting in algal bloom, loss of DO and aquatic species, and high turbidity. The case-controlled study assessed the efficiency of integrated use of aeration and phytoremediation for higher efficiency in improving several water quality parameters within 5 days in the laboratory setup. The reactor with water hyacinth and submerged aerators had greater ammonia–nitrogen (AN) conversion efficiency (93.9%), which was 2.3 times better than using only submerged aeration and 3 times better than natural aeration. The water quality also got better in terms of BOD, COD, TDS, and turbidity. The reactor with water hyacinth and submerged aerators was consistently seen to work very well. For better performance and further successful implications, a real-life, large-scale assessment is recommended.