The emplacement of large intrusive complexes into sedimentary basins can have profound effects on host sedimentary rocks including deformation, thermal aureole metamorphic reactions, alteration of fluid flow pathways, and the formation of associated hydrothermal vent complexes (HVCs). These processes can in turn have major implications for petroleum systems on the local and regional scale, and can contribute to global climate change due to the production and outgassing of greenhouse gases such as CH4 and CO2. Imaging these features and assessing their implications from seismic data beneath extrusive volcanic cover is challenging both due to heterogeneities in the volcanic pile and at the basalt sediment transition. In this study, we present combined field and laboratory petrophysical data from the Isle of Skye, Scotland, where we identify a seismic scale example of extensive intrusions interacting with the base-basalt transition. Within the study, we also document a unique onshore example of a linked sill and associated hydrothermal vent complex (HVC) cutting up through the lava sequence. We compare these field results to HVCs from reflection seismic data across the Voring Marginal High, offshore Norway, where sub-basalt saucer-shaped intrusions are also seen associated with HVCs cutting the lava sequence. Seismic imaging problems associated with the velocity heterogeneity of volcanic sequences, along with a historical lack of high quality 3D data in volcanic regions worldwide, is suggested as having largely precluded the identification of these features in the past. The under-representation of these hydrothermal vents in the literature has key implications for the future appraisal of intrusion-related outgassing effects on global climate such as those related to the Palaeocene Eocene Thermal Maximum (PETM), along with sub-basalt petroleum prospectivity where they may alter maturation and migration pathways.