The identification of preferential flow generation and the tracking of their pathways in agricultural soils are challenging tasks, in particular while keeping the soil profile undisturbed. The noninvasive electrical resistivity tomography (ERT) method seems, a priori, to be an ideal tool for these purposes, but the simultaneous dependence of soil electrical resistivity (ER) on soil moisture content and salt concentration poses a problem when high-salinity water is involved. The dependence of these variables is expressed, for example, by Archie’s law. Irrigation with brackish or treated wastewater are two such complicated cases. The latter has been found to render soils water-repellent with inherent flow in preferential pathways. A method that resolves this complication is developed and applied for in-situ-measured ERT data. This method combines a model that simulates the preferential ER(t) as a series of interconnected well-mixed units (WMUs) with frequent ERT scans during soil wetting and subsequent drying. Following validation by comparison of its output to simulations using the Richards equation for flow and convection-dispersion equation for transport, the WMU model was used to simulate scenarios of simultaneous variations in moisture content, salinity, and ER(t) in a well-mixed soil volume (unit). The characteristic patterns acquired by these simulations were compared with in-situ measured ER(z,t) to determine whether the observed preferential ER pathways coincide with preferential flow or salinity pathways, or both. From the eight sections in the profile where this analysis was made for, five exhibit preferential flow, characterized by fast wetting front propagation that includes by-passing of a certain soil volume, while the wetting front velocity in the other three was moderate. We, therefore, concluded, based on the water content/salinity effect on ER, that the measured preferential ER pathways coincide with preferential flow pathways. Salinity has, for the current case, a minor, if any, effect on the ER spatial variation. Therefore, ERT is an advantageous mean of mapping of preferential flow pathways in the soil profile, and the method developed herein can be used for studying the water distribution in the soil profile. Particular irrigation design and management can be then used to ease the negative effects of preferential flow pathways on soil water availability to plant roots and the enhanced leaching of agrochemical below the active root zone.