A large number of Calyptogena-dominated benthic communities, apparently chemosynthetically-based, were discovered at methane-rich pore-water seeps in the Japan subduction zones (3850–6000 m depth). Photographic and video surveys from four submersible dives were analyzed to study the influence of faulting, topography and substratum on exploitation of cold seeps by megafauna. Pore-water seepage occurred in a variety of geological settings, including subduction-erosion and accretionary prism formation, always in association with major faults which likely facilitated upward migration of fluids from a deep high-pressure zone. Sediment cover and manganese crusts on the seafloor appeared to block pore-water discharge, except where interrupted by erosion, slumping or outcropping. Sediment or mudstone substrata may increase lateral diffusion of rising fluids, permitting more extensive biological exploitation than where fluids discharge directly from exposed rock. Cold seeps are ephemeral. Large long-lived “fields” of cold seeps may be important in the maintenance of regional populations of seep organisms and the transfer of cold-seep productivity to the surrounding deep-sea ecosystem.