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Carbon dioxide (CO 2 ) supersaturation in lakes and rivers worldwide is commonly attributed to terrestrial–aquatic transfers of organic and inorganic carbon (C) and subsequent, in situ aerobic respiration. Methane (CH 4 ) production and oxidation also contribute CO 2 to freshwaters, yet this remains largely unquantified. Flood pulse lakes and rivers in the tropics are hypothesized to receive large inputs of dissolved CO 2 and CH 4 from floodplains characterized by hypoxia and reducing conditions. We measured stable C isotopes of CO 2 and CH 4 , aerobic respiration, and CH 4 production and oxidation during two flood stages in Tonle Sap Lake (Cambodia) to determine whether dissolved CO 2 in this tropical flood pulse ecosystem has a methanogenic origin. Mean CO 2 supersaturation of 11,000 ± 9,000 μ atm could not be explained by aerobic respiration alone. 13 C depletion of dissolved CO 2 relative to other sources of organic and inorganic C, together with corresponding 13 C enrichment of CH 4 , suggested extensive CH 4 oxidation. A stable isotope-mixing model shows that the oxidation of 13 C depleted CH 4 to CO 2 contributes between 47 and 67% of dissolved CO 2 in Tonle Sap Lake. 13 C depletion of dissolved CO 2 was correlated to independently measured rates of CH 4 production and oxidation within the water column and underlying lake sediments. However, mass balance indicates that most of this CH 4 production and oxidation occurs elsewhere, within inundated soils and other floodplain habitats. Seasonal inundation of floodplains is a common feature of tropical freshwaters, where high reported CO 2 supersaturation and atmospheric emissions may be explained in part by coupled CH 4 production and oxidation.