The efficient use of water in irrigated agricultural systems is of increasing importance given the changes in climatic patterns currently being experienced in the irrigated areas of the Murray-Darling Basin (MDB) in Australia. In previous research, electromagnetic (EM) induction instruments have been used to map the distribution of the clay content in those areas. However, describing their vertical extent and connectivity with groundwater tables or stratigraphic features such as paleochannels has not been studied adequately. One of the reasons for the paucity of research is the lack of suitable instrumentation or software to invert apparent conductivity (σa) data. The aim of this research is to demonstrate how DUALEM-421 equipment, which operates using electromagnetic induction theory, can be used to map not only the areal distribution of a prior stream channel but its vertical extent by inputting the data into a 1D spatially constrained algorithm for quasi-3D conductivity imaging. We discovered how the inversion of the apparent electrical conductivity, measured in the horizontal (HCP) and perpendicular (PRP) arrays, characterizes the Quaternary alluvial clays which dominate the riverine plain of the lower Gwydir valley, and indicates the location and extent of a prior stream channel and its sediments across Auscott Midkin field 11. We found the calculated conductivity values favorably represent the known stratigraphy of these physiographic units. Our results suggest the prior stream channel may be interconnected with a more extensive paleochannel.