The evolution of submarine pockmarks is often related to the ascent of fluid from the subsurface. For pockmarks located within the gas hydrate stability zone, methane oversaturation can result in the formation of gas hydrates in the sediment. A ca. 600 m‐wide sea floor depression in deep‐waters offshore Nigeria, Pockmark A, was investigated for distributions and quantities of shallow gas hydrates, origins of hydrocarbons and time elapsed since the last major fluid ascent event. For the first time, pressure coring of shallow sediments and drilling of more than 50‐m‐long cores with the sea floor drill rig MARUM‐MeBo70 were conducted in this pockmark.

Unusually high hydrate saturations of up to 51% of pore volume in the uppermost 2.5 meters of sediment in the pockmark center substantiate that deep‐water pockmarks are a relevant methane reservoir. Molecular and stable C and H isotopic compositions suggest that thermogenic hydrocarbons and secondary microbial methane resulting from petroleum biodegradation are injected into shallower sediments and mixed with primary microbial hydrocarbons.

Two independent pore water chloride and sulfate modeling approaches suggest that a major methane migration event occurred during the past one to two centuries. A rough sea floor topography within the pockmark most likely results from combined sediment removal through ascending gas bubbles, hydrate clogging and deflection of migration pathways, gas pressure build‐up, and hydrate sea floor detachment. This study shows for the first time the chronological interrelationship between gas migration events, hydrate formation and sea floor shaping in a deep‐sea pockmark.