Marine sediments host large amounts of methane (CH4), which is a potent greenhouse gas. Quantitative estimates for methane release from marine sediments are scarce, and a poorly constrained temporal variability leads to large uncertainties in methane emission scenarios. Here, we use 2-D and 3-D seismic reflection, multibeam bathymetric, geochemical, and sedimentological data to (I) map and describe pockmarks in the Witch Ground Basin (central North Sea), (II) characterize associated sedimentological and fluid migration structures, and (III) analyze the related methane release. More than 1,500 pockmarks of two distinct morphological classes spread over an area of 225 km2. The two classes form independently from another and are corresponding to at least two different sources of fluids. Class 1 pockmarks are large in size (>6 m deep, >250 m long, and >75 m wide), show active venting, and are located above vertical fluid conduits that hydraulically connect the seafloor with deep methane sources. Class 2 pockmarks, which comprise 99.5% of all pockmarks, are smaller (0.9–3.1 m deep, 26–140 m long, and 14–57 m wide) and are limited to the soft, fine-grained sediments of the Witch Ground Formation and possibly sourced by compaction-related dewatering. Buried pockmarks within the Witch Ground Formation document distinct phases of pockmark formation, likely triggered by external forces related to environmental changes after deglaciation. Thus, greenhouse gas emissions from pockmark fields cannot be based on pockmark numbers and present-day fluxes but require an analysis of the pockmark forming processes through geological time.