13Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in 14 global biogeochemical cycles, yet aquatic OM cycling remains poorly understood. Here, we 15 present the first work to explicitly test OM thermodynamics as a key regulator of aerobic 16 respiration, challenging long-held beliefs that organic carbon and oxygen concentrations are the 17 primary determinants of respiration rates. We pair controlled microcosm experiments with 18 ultrahigh-resolution OM characterization to demonstrate a clear relationship between OM 19 thermodynamic favorability and aerobic respiration under carbon limitation. We also 20 demonstrate a shift in the regulation of aerobic respiration from OM thermodynamics to nitrogen 21 content when carbon is in excess, highlighting a central role for OM thermodynamics in aquatic 22 biogeochemical cycling particularly in carbon-limited ecosystems. Our work therefore 23 illuminates a structural gap in aquatic biogeochemical models and presents a new paradigm in 24 which OM thermodynamics and nitrogen content interactively govern aerobic respiration. 25 26 27 3 Metabolism of organic matter (OM) in freshwater ecosystems plays a large role in global 28 biogeochemical cycles 1-3 , as freshwater ecosystems emit more than 2 Pg C yr -1 into the 29 atmosphere 4,5 . These emissions are largely dominated by contributions from river corridors 1,5,6 , 30 and within the river corridor, areas of groundwater-surface water mixing (hyporheic zones) have 31 a disproportionate impact on aerobic respiration 7-9 . Recent field observations have suggested that 32 OM chemistry, and in particular OM thermodynamics, are key to predicting aerobic respiration 33 in hyporheic zones 10-12 . If supported, these observations challenge a widespread paradigm that 34 organic carbon and oxygen concentrations are the primary determinants of aerobic respiration 35 rates and highlight a key source of model uncertainty. Yet, no work has provided direct evidence 36 for OM thermodynamics as a regulator of aerobic respiration in a controlled laboratory 37 environment. Demonstrating this behavior would identify mechanisms that drive field-based 38 phenomena and would enable key properties of OM to be represented in predictive models, 39 thereby contributing to reducing the uncertainty in modeling river corridor biogeochemical 40 cycling 13,14 . 41We use highly controlled aerobic microcosms, non-invasive dissolved oxygen consumption 42 rates, and ultrahigh-resolution OM characterization to investigate the role of OM chemistry in 43 determining aerobic respiration in hyporheic zone sediments. Based on field observations 10-12 , 44 we hypothesized that OM chemistry, including thermodynamic favorability and nitrogen (N) 45 content, would regulate aerobic respiration. Historically, investigations of thermodynamic 46 constraints on microbial metabolism have primarily focused on oxidation-reduction reactions 47 premise that using oxygen as the terminal electron acceptor provides sufficient energy ...