The diagnosis of external water intrusion in urban sewage systems under high water level operation during the dry season is an important supporting task for improving the operational efficiency of the system. By locking down the problem areas layer by layer as the main objective, an overall framework for the research on the diagnosis of external water intrusion is constructed with the analysis of water balance in water supply and drainage linkage and the manual water quality monitoring as the core. Taking the service scope of a municipal wastewater treatment plant (WWTP) in a southern city as the research area, the amount of external water intrusion in the service scope of each pumping station is evaluated. The manual water quality monitoring of key nodes in the pipeline network at different levels for the identified key areas is carried out. Through the on-site verification, analysis of water quality indicators, and comparison with the defect detection data of the existing pipelines, the locked points 3, 5, 7, 11, 19, 20 and 24 have external water intrusion due to defects in the upstream sewage pipeline. The reduced water conveying capacity caused by the pipeline defects in the study area exacerbates the high water level operation of the sewage system. The diagnostic method proposed for the external water intrusion in sewage system is efficient and economical, which can provide a reference for similar cities.