It is significant to monitor the leakage at the joints of the diaphragm walls of subway station foundation pits to check the weak links in the waterproof quality of the diaphragm wall structure. It is essential to take effective waterproof measurements timely to improve the overall waterproof quality of the diaphragm wall in the foundation pit to prevent accidents and reduce the operation and maintenance costs. This paper used ground penetrating radar (GPR) to detect the Lishan North Road Station section of Jinan Rail Transit Line R2 during construction. The abnormal waveform image is obtained after processing radar detection data with Reflexw software. This abnormal waveform image is used to identify the abnormal area. In order to accurately predict the location of leakage at the joint of diaphragm wall, MATLAB is used to calculate the average wave velocity amplitude and single channel signal of the electromagnetic wave velocity of geological radar at different mileages and draw the trend chart of average wave velocity amplitude with mileage and the corresponding relationship curve of electromagnetic wave amplitude and depth of radar. It is proposed that sudden changes in the area of the average wave velocity amplitude cause a change in the trend chart. Furthermore, the radar electromagnetic wave velocity amplitude curve is taken as the area where seepage may occur at the joints of the diaphragm wall, so as to determine the corresponding mileage and depth of the leakage area. On this basis, the grey correlation analysis for the analysis of the source of the water leakage at the joints of the diaphragm wall of the subway foundation pit is proposed. The research results show that the leakage water at the joints of the diaphragm wall of the subway foundation pit is not connected to the rivers around the foundation pit, which confirms that the construction of the subway station has not affected the groundwater resources around the station. The proposed approach has successfully predicted the location of the foundation pit leakage disaster and has been verified on the project site. The research results provide a reference for the monitoring and early warning of leakage at the joints of diaphragm walls in foundation pits with similar geological conditions.