Over the last three decades, multicomponent geophysical prospection has given a new perspective in the domain of inland archaeological prospection. However, the complexity and constantly evolving environmental regime encountered in the transition zones has so far limited the implementation of these technological advancements towards the understanding of the past dynamics in littoral and ultra‐shallow offshore environments. The main objective of this work is to appropriately adapt, test and validate the efficiency of diverse geophysical mapping and imaging methods for reconstructing the ancient built environment below a relatively thin water layer. The submerged prehistoric site of Lambayanna in Greece was used as an ‘open laboratory’ to explore in situ the resolving capabilities and limitations of marine three‐dimensional electrical resistivity tomography and multisensor magnetic gradiometry, as well as terrestrial ground‐penetrating radar. The geophysical mapping covered more than 4.4 hectares of the shallow marine and coastal part of the site with high spatial resolution. The data processing followed a specific flowchart to enhance the signal and the subsequent integrated analysis showed a number of candidate targets buried below the seabed, providing strong indications to support the hypothesis for the existence of an ancient submerged man‐made environment in the bay. The results demonstrate the complementary nature of applying multiple geophysical methods to under‐explored shallow offshore archaeological contexts in order to provide useful information for understanding the complex archaeological sites around the Mediterranean. The successful transfer of established geophysical methods into the ultra‐shallow aquatic environment comprises the major innovative aspect of this work. Thus, in view of climate change and the risks related to future sea‐level rise and erosion of low‐level coastal areas, the proposed research model can be integrated into a wider strategic framework for the sustainable management of coastal cultural resources.