Pockmarks are specific type of marine geological setting resembling craters or pits. They are considered surface expression of fluid flow in the marine subsurface. Pockmarks are widespread in the aquatic environment but the understanding of their formation mechanisms, relationship with marine macro- and micro-biota and their geochemistry remains limited. Despite numerous findings of these features in Irish waters they received little attention and remain poorly studied. In this work extensive geophysical data sets collected by the Irish National Seabed Survey and its successor the INFOMAR project as well in situ sediment samples were utilized to provide baseline information on the nature of some of these features, the processes they are fuelled by and their geochemical characteristics. Pockmarks from open shelf (Malin Shelf) and bay, fjord like environment (Dunmanus Bay) are compared and theories of their formation are formulated. Sediment from these features was extensively studied utilizing advanced geotechnical and geochemical tools to describe and quantify processes taking place in the subsurface. Organic matter was characterized on a molecular level by combined biomarker and advanced Nuclear Magnetic Resonance approach.