The Baltic Basin is known for its numerous Paleozoic hydrocarbon reservoirs. There is published evidence that hydrocarbons are leaking from the seafloor, however, little is known about the hydrocarbon migration pathways from Paleozoic source and reservoir rocks toward the seafloor and their escape structures. To investigate these processes, we utilize a new set of multibeam, parametric sediment sub‐bottom profiler and 2D seismic reflection data. The integrated analysis of seismic profiles, diffraction imaging and bathymetric maps allow to identify a hydrocarbon migration system within Silurian and Devonian strata that consists of layer parallel and updip migration beneath sealing layers, migration across seals along faults, and seafloor escape structures in form of elongated depressions. The general migration trend is directed updip, from the Paleozoic reservoirs below the southeastern Baltic Sea toward the Gotland Depression in the northwest. The locations of the hydrocarbon escape structures at the seafloor and their elongated shape are mainly controlled by the regional geological setting of outcropping Paleozoic layers. In addition, iceberg scouring may have facilitated hydrocarbon migration through the Quaternary deposits. The description of this hydrocarbon migration system fills the gap between the known reservoirs and the observed hydrocarbon accumulations and seepages. With regard to potential Carbon Capture and Storage projects, the identification of this hydrocarbon migration system is of great importance, as potential storage sites may be leaking.