Atmospheric methane (CH 4 ) concentrations have more than doubled in the past~250 yr, although the sources of this potent greenhouse gas remain poorly constrained. Freshwaters contribute~20% of natural CH 4 emissions, about half attributed to ebullition. Estimates remain uncertain as ebullition is stochastic, making measurements difficult, time consuming, and costly with current methods (e.g., floating chambers, funnel gas traps, and hydroacoustics). We present a novel approach to quantify basin-wide hypolimnetic CH 4 fluxes at the sediment level based on measurements of bubble gas content and modeling of dissolved pore-water gases. We show that the relative ebullition flux pathway can be resolved by knowledge of only bubble gas content. As sediment CH 4 production, diffusion, and ebullition are interrelated, the addition of a second observation allows closing the entire sediment CH 4 balance. Such measurements could include bubble formation depth, sediment diffusive fluxes, ebullition, sediment CH 4 production, or the hypolimnetic CH 4 mass balance. The measurement of bubble gas content is particularly useful for identifying local ebullitive hotspots and integrating spatial heterogeneity of CH 4 fluxes. Our results further revealed the crucial effect of water column depth, production rates, and hypolimnetic dissolved CH 4 concentrations on sediment CH 4 dynamics. Although we apply the model to cohesive sediments in an anoxic hypolimnion, the model can be applied to shallow, oxic settings by altering the CH 4 production rate curve to account for oxidation. Utilizing our approach will provide a deeper understanding of in-lake CH 4 budgets, and thus improve CH 4 emission estimates from inland freshwaters at the regional and global scales.