Atmospheric contributions of methane from Arctic wetlands during the Holocene are dynamic and linked to climate oscillations. However, long-term records linking climate variability to methane availability in Arctic wetlands are lacking. We present a multi-proxy ~12,000 year paleoecological reconstruction of intermittent methane availability from a radiocarbon-dated sediment core (LQ-West) taken from a shallow tundra lake (Qalluuraq Lake) in Arctic Alaska. Specifically, stable carbon isotopic values of photosynthetic biomarkers and methane are utilized to estimate the proportional contribution of methane-derived carbon to lake-sediment-preserved benthic (chironomids) and pelagic (cladocerans) components over the last ~12,000 years. These results were compared to temperature, hydrologic, and habitat reconstructions from the same site using chironomid assemblage data, oxygen isotopes of chironomid head capsules, and radiocarbon ages of plant macrofossils. Cladoceran ephippia from ~4,000 cal year BP sediments have δ13C values that range from ~−39 to −31‰, suggesting peak methane carbon assimilation at that time. These low δ13C values coincide with an apparent decrease in effective moisture and development of a wetland that included Sphagnum subsecundum. Incorporation of methane-derived carbon by chironomids and cladocerans decreased from ~2,500 to 1,500 cal year BP, coinciding with a temperature decrease. Live-collected chironomids with a radiocarbon age of 1,640 cal year BP, and fossil chironomids from 1,500 cal year BP in the core illustrate that ‘old’ carbon has also contributed to the development of the aquatic ecosystem since ~1,500 cal year BP. The relatively low δ13C values of aquatic invertebrates (as low as −40.5‰) provide evidence of methane incorporation by lake invertebrates, and suggest intermittent climate-linked methane release from the lake throughout the Holocene.