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Abstract Aquatic networks contribute greenhouse gases and lateral carbon (C) export from catchments. The magnitudes of these fluxes exceed the global land C sink but are uncertain. Resolving this uncertainty is important for understanding climate feedbacks. We quantified vertical methane (CH4) and carbon dioxide (CO2) emissions from lakes and streams, and lateral export of dissolved inorganic and organic carbon from a hemiboreal catchment for 3 yr. Lateral C fluxes dominated the total aquatic C flux. All aquatic C fluxes were disproportionately contributed from spatially restricted areas and/or short‐term events. Hence, consideration of local and episodic variability is vital. Temperature and runoff were the main temporal drivers for lake and stream C emissions, respectively. Whole‐catchment aquatic C emissions scaled linearly with these drivers within timeframes of stable land‐cover. Hence, temperature and runoff increase across Northern Hemisphere humid areas from climate change may yield proportional increases in aquatic C fluxes.