The magnetic resonance sounding (MRS) method is used for noninvasive one-dimensional assessment of aquifer structures, i.e., for estimating the vertical water content and hydraulic conductivity distributions in the saturated zone. So far, MRS interpretation schemes for estimating the hydraulic conductivity as a function of the saturation degree in the vadose zone have not been developed. In this study we developed a new inversion scheme for MRS to estimate the relative hydraulic conductivity Krel, which is the ratio of the unsaturated and saturated conductivities. The new approach is based on the Brooks-Corey parameterization (BCP) of the capillary fringe; that is, the water content distribution of the capillary fringe is considered to be equivalent to the water retention curve in equilibrium state. The BCP inversion directly provides estimates of Brooks-Corey parameters from MRS data, which allows for the calculation of Krel as a function of the saturation degree. In doing so, the water table must be given as a priori information for the MRS inversion. We tested the feasibility of this approach with a field example and its reliability and limitations with a set of synthetic models.