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Some of the highest density pockmark fields in the world have been observed on the northwest Australian continental shelf (>700/km2) where they occur in muddy, organic-rich sediment around carbonate banks and paleochannels. Here we developed a semi-automated method to map and quantify the form and density of these pockmark fields (~220,000 pockmarks) and characterise their geochemical, sedimentological and biological properties to provide insight into their formative processes. These data indicate that pockmarks formed due to the release of gas derived from the breakdown of near-surface organic material, with gas accumulation aided by the sealing properties of the sediments. Sources of organic matter include adjacent carbonate banks and buried paleochannels. Polychaetes biodiversity appears to be affected negatively by the conditions surrounding dense pockmark fields since higher biodiversity is associated with low density fields. While regional bi-directionality of pockmark scours corresponds to modelled tidal flow, localised scattering around banks suggests turbulence. This multi-scale information therefore suggests that pockmark scours can act as proxy for bottom currents, which could help to inform modelling of benthic biodiversity patterns.