Electromagnetic induction (EMI) techniques have been used to monitor bulk seasonal soil-crop apparent electrical conductivity (ECa) dynamics. Interpreting this information can be complicated by changes in the soil profile such as water content or nutrient leaching. Time domain reflectometry (TDR) measures localized soil EC; therefore, TDR can provide clarification to where in the soil profile the EC changes are taking place. The objective of this study was to determine whether surface or deep EC changes were driving the response measured by EMI during the crop season of a field amended with animal manure. Results indicate that seasonal soil-crop EC dynamics measured by EMI are primarily driven by surface (<0.2 m) changes as opposed to deeper (>0.9 m) changes. These changes appear to be the result of surface ionic dynamics caused by crop-soil interactions and not soil volumetric water content (θv), since no significant correlations were detected between θv and ECa for any treatment, depth or dipole orientation. These findings are consistent with others who reported the EMI signal was driven primarily by changes in nitrate concentration and not by soil water content. The results of this study clarify our understanding of the soil dynamics that drive the ECa response of a manure amended field. The ability to non-intrusively measure nutrient mineralization and crop uptake provides researchers with a powerful tool for understanding soil-crop interactions. Understanding the soil-crop dynamic will facilitate development of management practices for amending soil with manure while protecting the environment from unintended contamination.