Methanogenesis has traditionally been assumed to occur only in anoxic environments, yet there is mounting, albeit indirect, evidence of methane (CH 4 ) production in oxic marine and freshwaters. Here we present the first direct, ecosystem-scale demonstration of methanogenesis in oxic lake waters. This methanogenesis appears to be driven by acetoclastic production, and is closely linked to algal dynamics. We show that oxic water methanogenesis is a significant component of the overall CH 4 budget in a small, shallow lake, and provide evidence that this pathway may be the main CH 4 source in large, deep lakes and open oceans. Our results challenge the current global understanding of aquatic CH 4 dynamics, and suggest a hitherto unestablished link between pelagic CH 4 emissions and surface-water primary production. This link may be particularly sensitive to widespread and increasing human influences on aquatic ecosystem primary productivity.

Methane (CH4) emissions from aquatic systems should be coupled to CH4 production, and thus a temperature‐dependent process, yet recent evidence suggests that modeling CH4 emissions may be more complex due to the biotic and abiotic processes influencing emissions. We studied the magnitude and regulation of two CH4 pathways—ebullition and diffusion—from 10 shallow ponds and 3 lakes in Québec. Ebullitive fluxes in ponds averaged 4.6 ± 4.1 mmol CH4 m−2 d−1, contributing ∼56% to total (diffusive + ebullitive) CH4 emissions. In lakes, ebullition only occurred in waters < 3 m deep, averaging 1.1 ± 1.5 mmol CH4 m−2 d−1, and when integrated over the whole lake, contributed only 18% to 22% to total CH4 emissions. While pond CH4 fluxes were related to sediment temperature, with ebullition having a stronger dependence than diffusion (Q10, 13 vs. 10; activation energies, 168 kJ mol−1 vs. 151 kJ mol−1), the temperature dependency of CH4 fluxes from lakes was absent. Combining data from ponds and lakes shows that the temperature dependency of CH4 diffusion and ebullition is strongly modulated by system trophic status (as total phosphorus), suggesting that organic substrate limitation dampens the influence of temperature on CH4 fluxes from oligotrophic systems. Furthermore, a strong phosphorus‐temperature interaction determines the dominant emission pathway, with ebullition disproportionately enhanced. Our results suggest that aquatic CH4 ebullition is regulated by the interaction between ecosystem productivity and climate, and will constitute an increasingly important component of carbon emissions from northern aquatic systems under climate and environmental change.