In the years 2000 and 2001 we measured methane concentrations exceeding up to two orders of magnitude the equilibrium with the atmosphere in the water column on the SW-Spitsbergen continental shelf. This methane anomaly extended from its centre on the shelf westwards over the upper slope and eastwards well into the inner basins of the two southernmost Spitsbergen fjords, the Hornsundfjord and the van Mijenfjord. Methane concentrations and stable carbon isotopic ratios varied between 2 and 240 nM, and between -53‰ and -20‰ VPDB, respectively. Methane in high concentrations was depleted in 13C whereas in low concentrations δ13CCH4 values were highly variable. On the continental shelf we found that methane discharged from seeps on top of sandy and gravelly banks is isotopically heavier than methane escaping from troughs filled with silty and clayey sediments. These distinct isotopic signatures suggest that methane is gently released from several inter-granular seepages or micro-seepages widely spread over the shelf. A potential migration path for thermogenic or hydrate methane may be the Hornsund Fracture Zone, a south-north running reactivated fault system created by stretching of the continental crust. After discharge into the water column, local water currents fed by Atlantic water, coastal water, and freshwater outflows from the fjords further determine pathways and fate of the methane. We used δ18Owater and 222Rn data to trace origin and advection of the local water masses and water mixing processes. Methane spreads predominantly along pycnoclines and by vertical mixing. During transport methane is influenced simultaneously by oxidation and dilution, as well as loss into the atmosphere. Together these processes cause the spatial variability of the anomaly and heterogeneity in δ13CCH4 in this polar shelf environment. © 2005 Elsevier Ltd. All rights reserved.