Coastal groundwater flow is driven by an interplay between terrestrial and marine forcings. One of the distinguishing features in these settings is the formation of a freshwater lens due to the density difference between fresh and saline groundwater. The present study uses data collected on Sable Island, Canada—a remote sand island in the northwest Atlantic Ocean—to highlight the potential of exploiting freshwater lens geometry for calibration of numerical groundwater flow models in coastal settings. Three numerical three-dimensional variable-density groundwater flow models were constructed for different segments of the island, with only one model calibrated using the freshwater–saltwater interface derived from an electromagnetic geophysical survey. The other two (uncalibrated) models with the same parameterisation as the calibrated model successfully reproduced the interpreted interface depth and location of freshwater ponds at different parts of the island. The successful numerical model calibration, based solely on the geophysically derived interface depth, is enabled by the interface acting as an amplified version of the water table, which reduces the relative impact of the interpreted depth uncertainty. Furthermore, the freshwater–saltwater interface is far more inertial than the water table, making it less sensitive to short-term forcings. Such “noise-filtering” behaviour enables the use of the freshwater–saltwater interface for calibration even in dynamic settings where selection of representative groundwater heads is challenging. The completed models provide insights into island freshwater lens behaviour and highlight the role of periodic beach inundation and wave overheight in driving short-term water-table variability, despite their limited impact on the interface depth.