The Coorong is a shallow (typically 1.5 m) narrow coastal lagoon extending ~110 km parallel to the coastline, and forms an extensive wetland area of international significance. It is divided into two lagoons, the North and South lagoons. The northern lagoon section opens into the mouth of the Murray River and the southern lagoon section is essentially closed, being connected to the North Lagoon via a choke point. During periods of extended drought where there is no flooding to flush the lagoon system, hypersalinisation gradually increases, especially in the southern lagoon section where salinity may be in excess of four times that of seawater. A helicopter time-domain EM (TEM) system was flown along the Coorong, as extensive flood waters from Queensland (2010) were reaching the North Lagoon lowering the salinity. The derived bathymetry from TEM data was shown to be in fair agreement with known bathymetry in areas of high salinity. The conductivities of waters ranging from saline to hypersaline in the North Lagoon and upper half of the South Lagoon, and underlying sediment, was estimated from inversion of TEM data using the known water depth as a fixed parameter. The derived conductivity varied from ~1.6 S/m in the north of the North Lagoon to ~8–10 S/m at its southern end and in the South Lagoon. These values underestimate the known strong salinity gradient (~0.6 to ~13 S/m respectively) observed from a sparse distribution of fixed conductivity meters located in the Coorong. The application of AEM in this region is challenging because of the very large range of water conductivities and because the average water depths are comparable to the typical residuals between known depths and depths derived from AEM data in previous studies in Australian coastal waters. These results do however show that AEM has the potential to remotely map shallow water depths, and water conductivity gradients using known bathymetry to monitor hypersalinisation in these significant wetland areas where changes in the ecology have been linked to high salinity.