Residential districts dominated by limestone are likely to be impacted by undesirable groundwater seepage accidents. Such groundwater seepage can generally give rise to loss of life and property. To control groundwater seepage, increasingly accurate and reliable methods for surveying are becoming indispensable. We proposed a survey method to confirm groundwater sources and preferential flow paths in urban limestone-based residential districts via ground penetrating radar (GPR) and time domain electromagnetic method (TDEM). Firstly, we established the geophysical exploration plan after careful analysis of available hydrogeological survey data including terrain, stratum distribution and water table. Survey lines were designed parallel to existing urban roads and perpendicular to the ground. Next, we used GPR and TDEM to detect gravels in the permeable layer and water-rich regions in the aquifer. Drilling method was adopted for comparisons to resulting images. Finally, integrated interpretation indicated accurate measures of groundwater sources, main preferential flow paths and the preliminary classification of groundwater leakage risk in a study region. The feasibility and effectiveness of the GPR and TDEM survey method were verified in the hydrogeological survey at the Lingxiucheng Residential District in China, where a thick limestone layer existed and groundwater leakage accidents had occurred in basements of houses. The method had high reliability for limestone topographies and was improved to be an effective and low-cost solution to overcome physical limitations of existent buildings and traffic jams in urban areas. Therefore, our research can be extended to similar projects and related problems to help better map urban limestone-based residential districts and reduce groundwater seepage.