Sub-seabed gas is commonly associated with seabed depressions known as pockmarks—the main venting sites for hydrocarbon gases to enter the water column. Sub-seabed gas accumulations are characterized by acoustically turbid or opaque zones in seismic reflection profiles, taking the form of gas blankets, curtains or plumes. How the migration of sub-seabed gas relates to the origin and distribution of pockmarks in nearshore and fjordic settings is not well understood. Using marine geophysical data from Loch Linnhe, a Scottish fjord, we show that shallow sub-seabed gas occurs predominantly within glaciomarine facies either as widespread blankets in basins or as isolated pockets. We use geospatial ‘hot-spot’ analysis conducted in ArcGIS to identify clusters of pockmarks and acoustic (sub-seabed) profile interpretation to identify the depth to gas front across the fjord. By combining these analyses, we find that the gas below most pockmarks in Loch Linnhe is between 1.4 m and 20 m deep. We anticipate that this work will help to understand the fate and mobility of sedimentary carbon in fjordic (marine) settings and advise offshore industry on the potential hazards posed by pockmarked seafloor regions even in nearshore settings.