An accurate understanding of the fresh‐saline distribution of groundwater is necessary for effective groundwater management. Airborne electromagnetic (AEM) surveys offer a rapid and cost‐effective method with which to map this, offering valuable additional information about the subsurface. To convert AEM data into electric conductivity and ultimately groundwater salinity, an inversion is undertaken. A number of algorithms are available for this purpose; however, these are affected by significant uncertainty, owing to inherent nonunique characteristics of this process. The most commonly used inversion codes in hydrogeophysical studies were quantitatively tested using frequency domain AEM and ground data from the province of Zeeland, the Netherlands. These include UBC1DFM code and quasi‐2D laterally constrained inversions. Following an investigation of inversion parameter settings, data were inverted for four inversion methods and interpolated into 3‐D volumes. Using geological data and empirical electrical conductivity and water salinity relationships, each inversion was converted into groundwater electrical conductivity and split into fresh‐brackish‐saline regions. For groundwater volume estimates out of a total volume of 2.8 billion m3, a fresh groundwater estimate could differ by as much as 178 million m3, depending on the inversion used. The primary factor here was the choice of model smoothness, which was shown to affect the thickness of the brackish interval. Fresh‐brackish‐saline interfaces were consistently mapped with an accuracy of ~3 m, the brackish being the most accurately resolved. The few layer method was less successful at resolving smoothly varying salinity distributions but more successful at mapping the brackish interface at greater depth.