Electromagnetic induction (EMI) instruments provide rapid, noninvasive, and spatially dense data for characterization of soil and groundwater properties. Data from multi-frequency EMI tools can be inverted to provide quantitative electrical conductivity estimates as a function of depth. In this study, multi-frequency EMI data collected across an abandoned uranium mill site near Naturita, Colorado, USA, are inverted to produce vertical distribution of electrical conductivity (EC) across the site. The relation between measured apparent electrical conductivity (EC_a) and hydraulic conductivity (K) is weak (correlation coefficient of 0.20), whereas the correlation between the depth dependent EC obtained from the inversions, and K is sufficiently strong to be used for hydrologic estimation (correlation coefficient of − 0.62). Depth-specific EC values were correlated with co-located K measurements to develop a site-specific ln(EC)–ln(K) relation. This petrophysical relation was applied to produce a spatially detailed map of K across the study area. A synthetic example based on EC_a values at the site was used to assess model resolution and correlation loss given variations in depth and/or measurement error. Results from synthetic modeling indicate that optimum correlation with K occurs at ~ 0.5 m followed by a gradual correlation loss of 90% at 2.3 m. These results are consistent with an analysis of depth of investigation (DOI) given the range of frequencies, transmitter–receiver separation, and measurement errors for the field data. DOIs were estimated at 2.0 ± 0.5 m depending on the soil conductivities. A 4-layer model, with varying thicknesses, was used to invert the EC_a to maximize available information within the aquifer region for improved correlations with K. Results show improved correlation between K and the corresponding inverted EC at similar depths, underscoring the importance of inversion in using multi-frequency EMI data for hydrologic estimation.