Gas hydrate and free gas accumulation in heterogeneous marine sediment is simulated using a two-dimensional (2-D) numerical model that accounts for mass transfer over geological timescales. The model extends a previously documented one-dimensional (1-D) model such that lateral variations in permeability (k) become important. Various simulations quantitatively demonstrate how focused fluid flow through high-permeability zones affects local hydrate accumulation and saturation. Simulations that approximate a vertical fracture network isolated in a lower permeability shale (kfracture >> kshale) show that focused fluid flow through the gas hydrate stability zone (GHSZ) produces higher saturations of gas hydrate (25–70%) and free gas (30–60%) within the fracture network compared to surrounding shale. Simulations with a dipping, high-permeability sand layer also result in elevated saturations of gas hydrate (60%) and free gas (40%) within the sand because of focused fluid flow through the GHSZ. Increased fluid flux, a deep methane source, or both together increase the effect of flow focusing upon hydrate and free gas distribution and enhance hydrate and free gas concentrations along the high-permeability zones. Permeability anisotropy, with a vertical to horizontal permeability ratio on the order of 10−2, enhances transport of methane-charged fluid to high-permeability conduits. As a result, gas hydrate concentrations are enhanced within these high-permeability zones. The dip angle of these high-permeability structures affects hydrate distribution because the vertical component of fluid flux dominates focusing effects. Hydrate and free gas saturations can be characterized by a local Peclet number (localized, vertical, focused, and advective flux relative to diffusion) relative to the methane solubility gradient, somewhat analogous to such characterization in 1-D systems. Even in lithologically complex systems, local hydrate and free gas saturations might be characterized by basic parameters (local flux and diffusivity).