Increased interest in the character of sediments at the base of waterways, for the purpose of managing river salinization, has led to the application of several geophysical techniques for collecting information from this zone. These instream methods are based on established ground and airborne electrical and electromagnetic technologies, including towed transient electromagnetic systems, towed direct current resistivity array systems, and frequency-domain helicopter electromagnetic systems. Although these systems are individually successful, a systematic examination of their relative effectiveness for identifying variations in substrate conductivity for a common stretch of a river remains lacking. We have compared results obtained from data collected using three instream geophysical techniques for a common stretch of the Murray River in southeastern Australia. The Murray River is an important water resource for drinking and agricultural purposes. Data from these surveys were acquired tolocate areas of significant saltwater accession to the Murray from a saline regional groundwater system that discharges into it. The three methods indirectly inform on those reaches that most likely contribute to higher salt loads in the river, and they do this through the identification of a conductive substrate (a gaining reach). For a stretch of the river, the methods identified similar variations in the conductivity structure of sediment substrate, although differences were observed in the modeled response relating to intrinsic differences between each system, including the sampling interval and resolution. The helicopter electromagnetic (EM) system is capable of acquiring hundreds of kil-ometers of data in a day, under any river flow condition, from near the river surface to depths in excess of . The other two techniques require safe river flow conditions for acquisition, with as much as 50 river km of data per day possible. The ground-based methods had enhanced lateral and vertical resolving capabilities relative to the helicopter EM system, but their depth of investigation was less (usually only ).