All geophysical inverse problems cannot be solved using the smoothness regularization, especially in the detection of sharp boundaries. Therefore, It’s necessary to use additional subsurface information such as other geophysical methods as a priori information. In this study, we proposed a structural constraint by velocity analysis of Ground Penetrating Radar (GPR) data and combining Topp’s and Archie’s formula for inversion of radio-magnetotelluric (RMT) data. Then, a profile with the length of 320 m was investigated on a known aquifer situated to the north of Heby, Sweden. The inversion result of RMT data using the proposed constraint yields better results than the constrained inversion utilizing the common-offset (CO) section. Also, both methods provide far better results than the standard smoothness constraint. Such that the water table at a depth of less than 20 m, and consequently the saturated zone is detected well, and the result correlates to the available subsurface information.