AbstractSmall island communities often rely on groundwater as their primary source of fresh water. However, the limited land area and high proportion of coastal zones pose unique challenges to groundwater management. A detailed understanding of the subsurface structure can provide valuable insights into aquifer structure, groundwater vulnerability, saltwater intrusion, and the location of water resources. These insights can guide groundwater management strategies, for example, pollution regulation, promotion of sustainable agriculture, establishment of coastal buffer zones, and re‐naturalization of land cover. Ordinarily, structural characterization relies on geological mapping and boreholes, however, such approaches can have insufficient spatial resolution to aid groundwater management. In this study, transient electromagnetic (TEM) methods are used to map the subsurface of a small, 13.2 km2, Danish Island. The approach successfully identified two previously unknown paleochannels, where the interface between Quaternary aquifer units and an underlying Paleogene Clay aquiclude had maximum depths of 100 and 160 m below sea level. Before this, the interface was assumed to be 15 to 25 m below sea level: therefore, these paleochannels present substantial potential groundwater resources. Resolving geological heterogeneity within the Quaternary deposits was less successful and future work will focus on addressing these limitations. Nonetheless, in several locations, evidence of saltwater intrusion was observed within the Quaternary units. This work demonstrates how TEM mapping can identify water resources, define aquifer boundaries, and aid water management decisions. Such approaches could be applied in other areas, particularly small islands, where similar groundwater challenges exist.