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Helicopter time-domain airborne electromagnetic (AEM) methodology is being investigated as a reconnaissance technique for bathymetric mapping in shallow coastal waters, especially in areas affected by water turbidity where light detection and ranging (LIDAR) and hyperspectral techniques may be limited. Previous studies in Port Lincoln, South Australia, used a floating AEM time-domain system to provide an upper limit to the expected bathymetric accuracy based on current technology for AEM systems. The survey lines traced by the towed floating system were also flown with an airborne system using the same transmitter and receiver electronic instrumentation, on two separate occasions. On the second occasion, significant improvements had been made to the instrumentation to reduce the system self-response at early times. A comparison of the interpreted water depths obtained from the airborne and floating systems is presented, showing the degradation in bathymetric accuracy obtained from the airborne data. An empirical data correction method based on modelled and observed EM responses over deep seawater (i.e. a quasi half-space response) at varying survey altitudes, combined with known seawater conductivity measured during the survey, can lead to significant improvements in interpreted water depths and serves as a useful method for checking system calibration. Another empirical data correction method based on observed and modelled EM responses in shallow water was shown to lead to similar improvements in interpreted water depths; however, this procedure is notably inferior to the quasi half-space response because more parameters need to be assumed in order to compute the modelled EM response. A comparison between the results of the two airborne surveys in Port Lincoln shows that uncorrected data obtained from the second airborne survey gives good agreement with known water depths without the need to apply any empirical corrections to the data. This result significantly decreases the data-processing time thereby enabling the AEM method to serve as a rapid reconnaissance technique for bathymetric mapping.