The Bet She’an and Harod Valleys are regional recipients and mixing zones for groundwater draining to these valleys from a multiple aquifer system. This aquifer system includes two different carbonate aquifers, several groundwater-bearing basalt flows and deep-seated pressurized brine, the upflow of which causes salinization of fresh groundwater bodies. These aquifers drain through two groups of springs. Due to lack of information on the subsurface structure of the valley the flow-paths of groundwater feeding the springs, the initial distribution of salinities along the valley and particularly, the inflow-paths of the brines, have never been understood but were assumed to be fault-controlled. The interpretation of seismic profiles and analysis of gravity anomalies revealed the subsurface structure of the valley and namely the occurrence of a dense network of faults which branch out from those delineating the Jordan-Dead Sea Rift. The faults formed a series of uplifted and down-warped horst-and-graben structures. By joint analysis of structural, hydrological and geochemical evidence, it occurs that groundwater flow-paths leading to the springs emerging in the middle of the Bet She’an Valley are determined by structural elements such as major faults and fault-controlled structures. The penetration of the pressurized Ca-chloride Rift brines and their inflow into fresh groundwater bodies occurs prevalently along the faults outlining the western margins of the Dead Sea Rift Valley and at their intersection with outbranching NW–SE-striking faults.