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The Western Continental Shelf of India experiences water-column anoxia during late summer/early autumn, thereby providing conducive conditions for methane (CH 4) accumulation. Measurements of CH4 along with other ancillary physico-chemical variables were made during the period of anoxia (September–October) in 2003, 2005 and 2009. The shelf waters experienced variable oxygen deficiency (hypoxic to anoxic) in space and time. Maximum observed accumulation of CH4 was only ~104 nmol/L although the bottom waters were strongly reducing with hydrogen sulphide (H 2S) concentration reaching up to 26.6 μmol/L. Methane showed a reasonable positive correlation with H2S. The observed CH4 accumulation over the Indian shelf was lower than previously reported from the major Eastern Boundary Upwelling systems, especially off Namibia. It is proposed that the low organic loading arising from lower productivity and consequently weak sedimentary methanogenesis may largely account for the lower CH 4 concentrations in anoxic bottom waters over the Indian shelf. Also, while anoxia may limit CH4 oxidation, sedimentary inputs are probably a more important source of water column CH4. In spite of the moderate CH4 build up in bottom waters, CH4 saturation at the sea-surface observed in the present study (89–1041%) was relatively lower than observed in 1996–1997 (~110–2521%). The sea to air flux of CH4 ranged from −0.52 to 26.56 μmol m−2 d−1, marginally higher than previously reported from the upwelling system in the western Arabian Sea.