The Federal Institute for Geosciences and Natural Resources (BGR) conducted many airborne geophysical surveys in Northern Germany during the last decades. The coastal regions of Lower Saxony were investigated by frequency-domain helicopter-borne electromagnetics (HEM) to reveal the bulk resistivity of the subsurface (sediments and pore fluids). The State Authority for Mining, Energy and Geology (LBEG) is preparing a statewide “saltwater map” for Lower Saxony with a focus on the coastal aquifers influenced by seawater intrusion. For this purpose, the HEM resistivities are used in combination with groundwater data and a geological model to derive the lower fresh-water boundary. As appropriate depth values are manually picked from vertical resistivity sections, this procedure is time consuming. Therefore, we tested an alternative, which automatically derives the fresh-saline groundwater boundary directly from the HEM resistivity models. The ambiguity between brackish/saline water and clayey sediments as source for low resistivities can somewhat be reduced by the application of gradients instead of threshold values for searching an appropriate boundary. We compare results of both methods using a dataset from a coastal region at the Jade Bay.