Latent heat polynyas are regions generating strong ice formation, convection and extensive water mass formation. Here we report on the effects of these processes on resuspension of sediments and subsequent methane release from the seafloor and on the resulting excess methane concentration in surface water on a polar shelf during winter. The study is based on measurements of concentration and δ13C values of methane, water temperature, salinity, light transmission and sea ice data collected in March 2003 in Storfjorden, southern Svalbard. In winter, strong and persistent northeasterly winds create polynyas in eastern Storfjorden and cause ice formation. The resulting brine-enriched water cascades from the Storfjordbanken into the central depression thereby enhancing the turbulence near the seafloor. A distinct benthic nepheloid layer was observed reflecting the resuspension of sediments by the cascading dense bottom water. High concentrations of 13C-depleted methane suggest submarine discharge of methane with the resuspended sediments. As the source of the submarine methane, we propose recent bacterial methanogenesis near the sediment surface because of extremely high accumulation rates of organic carbon in Storfjorden. Convective mixing transports newly released methane from the bottom to the sea surface. This eventually results in an excess concentration in surface water with respect to the atmospheric equilibrium, and a sea-air flux of methane during periods of open water. When a new ice cover is formed, methane becomes trapped in the water column and subsequently oxidized. Thus, the residual methane is strongly enriched in 13C in relation to the δ13CCH4δ13CCH4 signature of atmospheric methane. Our results show that latent heat polynyas may induce a direct pathway for biogases like methane from sediments to the atmosphere through coupling of biogeochemical and oceanographic processes. Extrapolating these processes to all Arctic ocean polynyas, we estimate a transfer of CH4 between 0.005 and 0.02 Tg yr−1. This is not a large contribution but the fluxes from the polynyas are 20–200 times larger than the ocean average and the methane evasion process in polynyas is certainly one that can be altered under climate change.