An electrical resistivity and electromagnetic emission survey was carried out involving the use of vertical electrical soundings (VES) and natural pulse electromagnetic field of the earth (NPEMFE). The use of this new methodology managed to detect the fracture flow system rupture zones in the underground, also answered the questions about the deferent subsurface water bodies. The present study focuses on Marsaba-Feshcha sub-basin in the northeast of the Dead Sea. Due to the scarcity of boreholes in the study area, several geophysical methods were implanted. The combination of these two methods (VES and NPEMFE) with the field observations and East-West transversal faults with the coordination (624437/242888) was determined, cutting through the anticlines with their mainly impervious cores with fracture length of >400 m. These transversal faults saddle inside Nabi Musa syncline (Boqea syncline), leading to a hydraulic connection between the Lower and the Upper Aquifer. Due to the identified transversal fault, the water of the Upper and Lower Aquifer mixed and emerged as springs at Ein Feshcha group.