Hydrocarbon prospectivity in the Greater Barents Sea remains enigmatic as gas discoveries have dominated over oil in the past three decades. Numerous hydrocarbon-related fluid flow anomalies in the area indicate leakage and redistribution of petroleum in the subsurface. Many questions remain unanswered regarding the geological driving factors for leakage from the reservoirs and the response of deep petroleum reservoirs to the Cenozoic exhumation and the Pliocene-Pleistocene glaciations. Based on 2D and 3D seismic data interpretation, we constructed a basin-scale regional 3D petroleum systems model for the Hammerfest Basin (1 km × 1 km grid spacing). A higher resolution model (200 m × 200 m grid spacing) for the Snøhvit and Albatross fields was then nested in the regional model to further our understanding of the subsurface development over geological time. We tested the sensitivity of the modeled petroleum leakage by including and varying fault properties as a function of burial and erosion, namely fault capillary entry pressures and permeability during glacial cycles. In this study, we find that the greatest mass lost from the Jurassic reservoirs occurs during ice unloading, which accounts for a 60%–80% reduction of initial accumulated mass in the reservoirs. Subsequent leakage events show a stepwise decrease of 7%–25% of the remaining mass from the reservoirs. The latest episode of hydrocarbon leakage occurred following the Last Glacial Maximum (LGM) when differential loading of Quaternary strata resulted in reservoir tilt and spill. The first modeled hydrocarbon leakage event coincides with a major fluid venting episode at the time of a major Upper Regional angular Unconformity (URU, ~0.8 Ma), evidenced by an abundance of pockmarks at this stratigraphic interval. Our modelling results show that leakage along the faults bounding the reservoir is the dominant mechanism for hydrocarbon leakage and is in agreement with observed shallow gas leakage indicators of gas chimneys, pockmarks and fluid escape pipes. We propose a conceptual model where leaked thermogenic gases from the reservoir were also locked in gas hydrate deposits beneath the base of the glacier during glaciations of the Hammerfest Basin and decomposed rapidly during subsequent deglaciation, forming pockmarks and fluid escape pipes. This is the first study to our knowledge to integrate petroleum systems modelling with seismic mapping of hydrocarbon leakage indicators for a holistic numerical model of the subsurface geology, thus closing the gap between the seismic mapping of fluid flow events and the geological history of the area.