The complexity of organic matter (OM) degradation mechanisms represents a significant challenge for developing biogeochemical models to quantify the role of aquatic sediments in the climate system. The common representation of OM by carbohydrates formulated as CHO in models comes with the assumption that its degradation by fermentation produces equimolar amounts of methane (CH) and dissolved inorganic carbon (DIC). To test the validity of this assumption, we modeled using reaction-transport equations vertical profiles of the concentration and isotopic composition (δC) of CH and DIC in the top 25 cm of the sediment column from two lake basins, one whose hypolimnion is perennially oxygenated and one with seasonal anoxia. Our results reveal that methanogenesis only occurs via hydrogenotrophy in both basins. Furthermore, we calculate, from CH and DIC production rates associated with methanogenesis, that the fermenting OM has an average carbon oxidation state (COS) below −0.9. Modeling solute porewater profiles reported in the literature for four other seasonally anoxic lake basins also yields negative COS values. Collectively, the mean (±SD) COS value of −1.4 ± 0.3 for all the seasonally anoxic sites is much lower than the value of zero expected from carbohydrates fermentation. We conclude that carbohydrates do not adequately represent the fermenting OM and that the COS should be included in the formulation of OM fermentation in models applied to lake sediments. This study highlights the need to better characterize the labile OM undergoing mineralization to interpret present-day greenhouse gases cycling and predict its alteration under environmental changes.