The terrain of the southern plain river network cities is flat and low-lying, and the water system is well-developed, which means the drainage capacity of the pipelines is greatly affected by the water level of the water system. Due to their unique geographical environment, these cities face dual challenges in wastewater treatment and water resource management. With the acceleration of urbanization, the volume of wastewater discharge continues to increase. Facing new situations such as carbon peak and carbon neutrality, pollution reduction and carbon emission reduction synergistic efficiency, and new pollutant control, traditional wastewater treatment methods can no longer meet the growing environmental demands. This paper analyzes the characteristics of the drainage system and the current situation of the wastewater system in southern plain river network cities, and combs the challenges faced by the wastewater system, such as external water intrusion, serious backflow of river and lake water, high water level operation, serious overflow pollution during the rainy season, and low influent water quality concentration. Based on this, targeted measures such as lowering water levels to inspect the sewage network, municipal network system rectification, drainage unit rectification, and optimizing the operation of the sewage network are proposed to improve the quality and efficiency of wastewater in southern plain river network cities. This is expected to provide suggestions, ideas, and references for the work of improving the quality and efficiency of wastewater in southern plain river network cities.