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Geostatistical modeling, using airborne and borehole electromagnetic data, was used to estimate electrical conductivity in groundwater within fractured paragneisses and migmatites in a semi-arid climate in northeastern Brazil. Despite the geologic heterogeneity of crystalline aquifers, the use of high resolution helicopter electromagnetic (HEM) data enabled the characterization of groundwater electrical conductivity where data from drilled wells were insufficient. The tacit assumption is that HEM measurements can be used to relate rock electrical conductivity to groundwater electrical conductivity. In this study, the HEM data were used as an external drift variable in non-stationary estimation and stochastic simulation to identify the variability of groundwater electrical conductivity. Validation tests, comparing predicted values for groundwater conductivity with measurements in new wells, confirmed the success of these models in locating fresh groundwater sources in crystalline bedrock.