Water pollution disrupts the ecological integrity of urbanized river systems, but its impacts on riverine metabolic processes and carbon fluxes are poorly studied in developing countries. Three seasonal field surveys were combined with two high-resolution measurements and an in situ incubation experiment to investigate the effects of untreated wastewater on organic matter biodegradation and the partial pressure of CO2 (pCO2) along the Mekong–Tonle Sap network around Phnom Penh. High-resolution measurements during the dry-season survey exhibited large downstream increases in pCO2 along the Mekong reaches receiving Tonle Sap inflows carrying urban sewage, contrasting with little spatial variation during a monsoon survey when the Mekong floodwater reversed the Tonle Sap flow. The monsoonal and dry-season surveys revealed flooding-induced homogenization and large spatial divergences in dissolved organic carbon (DOC) concentration and its δ13C and Δ14C between the Tonle Sap and connected Mekong reaches. During the 3-day incubation of Mekong waters, alone or mixed with sewage, a large initial nocturnal increase in pCO2 in sewage-supplemented river water exceeded the subsequent daytime CO2 uptake by phytoplankton photosynthesis varying with light exposure. This, combined with the preferential consumption of labile DOC components displaying protein-like fluorescence, implies sewage-enhanced biodegradation of riverine organic matter. These results suggest that neglecting wastewater-enhanced CO2 production in urbanized river basins during long dry periods can result in a significant underestimation of riverine CO2 emissions.