Pollution of urban rivers not only destroys the river ecology but also adversely affects the health of residents and urban landscape. In this regard, we selected a certain river in Wuhan for research. In this paper, we utilize the modified bypass multi-stage ecological pond reservoir system, set up the front parthenogenetic pond, aeration and oxygenation pond, ecological purification pond and other processes, supplemented with aeration–bacteriophage coupling, filler-type ecological floating island and other technologies to improve the water quality of the river. Results show that 4 months after the operation of the system, the rate of enhancement in water transparency reached 550%, and with a dissolved oxygen (DO) uplift rate of 322%, in addition, this system achieved 77.98, 77.78 and 74.41% removal of the ammonia nitrogen (NH3-N), total phosphorus (TP), chemical oxygen demand (COD) respectively, and the effluent water quality meets the target water quality standard. The process not only has a good pollutant removal effect, low cost and other characteristics but also can enhance the river landscape and improve biodiversity. It can provide a reference for similar river pollution water quality improvement.