Soil salinization is of great concern in the irrigated arid and semi-arid western United States due to its threat to sustainable agricultural productivity and thus is closely monitored. A widely accepted and traditional standard method for estimating soil salinity is the electrical conductivity of the saturated paste extracts (ECe). However, this method underestimates salinity due to ion pair formation in high ionic strength solution. Numerous studies have recommended the use of an electromagnetic induction (EMI) sensing technique to monitor field-scale soil salinity due to rapidness and non-destructiveness of the sampling. However, because the EMI measurement (ECa) is related to a host of soil properties, calibrating ECa to salinity in a non-homogeneous setting is particularly challenging. The main objective of this study is to understand the dynamics and interacting factors controlling soil salinity using an EMI sensor. Specifically, a correction is made for the underestimation of soil salinity from saturated paste extracts, and a calibration model is developed that is capable of predicting salinity directly from ECa despite the non-homogeneity of potential perturbing factors. A comparison is made of salinity measurement methods based on soil saturated pastes with respect to specific soil management goals. Results show that ion pairing exists even in low ionic strength solution and by diluting the saturated paste extracts to conductivities ≤ 0.03 dS m -1 (ECed), ion pairing is minimized. An improved salinity estimate is obtained by computing total dissolved solids (TDS, in mM) from the ECed values, and then multiplying the TDS by the dilution factor. We also developed a calibration model using quantile regression, which makes no assumption about the distribution of the errors, and which is capable of predicting low range soil salinity (such as that in calcareous soils) from ECa depth-weighted measurements (ECH25ECe). A comparison of ECe, ECed, ECH25ECe, and direct measurement of EC in soil pastes (“ Bureau of Soils Cup ” method, ECcup) across six depths, three texture groups, and the combinations of EC method and depth or texture groups, supports the use of the ECH25ECe method to rapidly and reliably monitor salinity in calcareous soils of arid and semiarid regions.