We analyzed the processes affecting the methane (CH4) budget in Lake Kinneret, a deep subtropical lake, using a suite of three models: (1) a bubble model to determine the fate of CH4 bubbles released from the sediment; (2) the one-dimensional physical lake model Simstrat to calculate the mixing dynamics; and (3) a biogeochemical model implemented in Aquasim to quantify the CH4 sources and sinks. The key pathways modeled include diffusive and bubble release of CH4 from the sediment, aerobic CH4 oxidation, and atmospheric gas exchange. The temporal and spatial dynamics of dissolved CH4 concentrations observed in the lake during 3 years could be well represented by the combined models. Remarkably, the relative contributions of ebullition and diffusive transport to the accumulation of CH4 in the hypolimnion during the stratified period could not be accurately constrained based only on the observed evolution of CH4 concentrations in the water column. Importantly, however, our analysis showed that most (∼99%) of the CH4 supplied to the water column by bubble dissolution and diffusive transport from the sediment is aerobically oxidized, whereas a substantial fraction (∼60%) of the sediment-released bubble CH4 is directly transported to the atmosphere. Ebullition is thus responsible for the bulk of the emissions from Lake Kinneret to the atmosphere. Therefore, as in all freshwaters, ebullition quantification is crucial for accurately assessing CH4 emissions to the atmosphere. This task remains challenging due to high spatio-temporal variability, but combining in situ measurements with a process-based modeling can help to better constrain flux estimates.