Methane seepage at south Hydrate Ridge (offshore Oregon, United States), one of the best-studied examples of gas venting through gas hydrates, is the seafloor expression of a vigorous fluid flow system at depth. The seeps host chemosynthetic ecosystems and release significant amounts of carbon into the ocean. With new three-dimensional seismic data, we image strata and structures beneath the ridge in unprecedented detail to determine the geological processes controlling the style of focused fluid flow. Numerical fluid flow simulations reveal the influence of free gas within a stratigraphic unit known as Horizon A, beneath the base of gas hydrate stability (BGHS). Free gas within Horizon A increases the total mobility of the composite water-gas fluid, resulting in high fluid flux that accumulates at the intersection between Horizon A and the BGHS. This intersection controls the development of fluid overpressure at the BGHS, and together with a well-defined network of faults, reveals the link between the gas hydrate system at depth and methane seepage at the surface.