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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 …