Groundwater discharge from the seasonally thawed active layer is increasingly recognized as an important pathway for delivering methane (CH4) into Arctic lakes and streams, but its contribution to CH4 emissions from thaw ponds and its influence on the trophic support and nutritional quality of pond food chains remains unexplored. We quantified the transport of CH4 from the active layer through groundwater discharge into thaw ponds in a subarctic catchment in northern Sweden, using radon (222Rn) as groundwater tracer. We analyzed stable isotopes and fatty acids of pond macroinvertebrates to evaluate the potential effects of groundwater-mediated CH4 inputs on the aquatic food chains. Our results indicate that active layer groundwater discharge flows are nontrivial (range 6%–46% of pond volume per day) and the associated CH4 fluxes (median 339 mg C m−2day−1, interquartile range [IQR]: 179–419 mg C m−2 day−1) can sustain the diffusive CH4 emissions from most of the ponds (155 mg C m−2 day−1, IQR: 55–234 mg C m−2 day−1). Consumers in ponds receiving greater CH4 inputs from the active layer had lower stable carbon (C) isotope signatures that indicates a greater trophic reliance on methane oxidizing bacteria (MOB), and they had lower nutritional quality as indicated by their lower tissue concentrations of polyunsaturated fatty acids. Overall, this work links physical (CH4 transport from the active layer), biogeochemical (CH4 emission), and ecological (MOB-consumer interaction) processes to provide direct evidence for the role of active layer groundwater discharge in CH4 cycling of subarctic thaw ponds.