Fluid seepages and seabed pockmarks are widely observed on continental margins worldwide in hydrate- and non-hydrate-bearing sediment. Subsurface gas chimneys connecting seafloor pockmarks to underlying gas reservoirs are commonly revealed by seismic reflection data, indicating pathways of past and present fluid migration. Fluid seepage occurs when the seal of a gas reservoir is breached, allowing fluids to migrate upward and vent at the seafloor, forming pockmarks. In hydrate-bearing settings, gas reservoirs beneath hydrate layers typically consist of coexisting water and gas phases. However, quantitative constraints on gas saturation in free-gas zones beneath hydrates inferred from pockmark morphology remain limited. In this study, a two-phase pockmark model was developed to investigate gas-chimney growth and pockmark formation, and to estimate gas saturation in free-gas zones below hydrates using pockmark depth and gas-zone thickness as key parameters. The model was applied to the Storegga Slide region off Norway, where hydrates, pockmarks, and chimney-like seismic anomalies have been documented. Here, the application is intended to represent localized near-threshold (pre-seepage) conditions leading to pockmark initiation, rather than the present-day post-venting state. Model results for the initiation (near-threshold, pre-venting) stage indicate that the effective gas saturation in the free-gas reservoir beneath the hydrates was approximately 1.36–1.58% for gas-zone thicknesses of 50–100 m, and that the corresponding chimney-propagation timescale during initiation was on the order of ~200 years. These estimates represent threshold conditions required for seal breach and pockmark formation rather than present-day seepage states. During venting, methane gas may form hydrates within the chimney inside the hydrate stability zone, while authigenic carbonates precipitate in pockmarks and shallow sediments. These secondary hydrates and carbonates eventually seal the chimney, leaving behind a residual gas chimney in the subsurface sediment.