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Shallow seabed depressions attributed to focused fluid seepage, known as pockmarks, have been documented in all continental margins. In this study, we demonstrate how pockmark formation can be the result of a combination of multiple factors—fluid type, overpressures, seafloor sediment type, stratigraphy and bottom currents. We integrate multibeam echosounder and seismic reflection data, sediment cores and pore water samples, with numerical models of groundwater and gas hydrates, from the Canterbury Margin (off New Zealand). More than 6800 surface pockmarks, reaching densities of 100 per km2, and an undefined number of buried pockmarks, are identified in the middle to outer shelf and lower continental slope. Fluid conduits across the shelf and slope include shallow to deep chimneys/pipes. Methane with a biogenic and/or thermogenic origin is the main fluid forming flow and escape features, although saline and freshened groundwaters may also be seeping across the slope. The main drivers of fluid flow and seepage are overpressure across the slope generated by sediment loading and thin sediment overburden above the overpressured interval in the outer shelf. Other processes (e.g. methane generation and flow, a reduction in hydrostatic pressure due to sea‐level lowering) may also account for fluid flow and seepage features, particularly across the shelf. Pockmark occurrence coincides with muddy sediments at the seafloor, whereas their planform is elongated by bottom currents. [ABSTRACT FROM AUTHOR]