Waterborne carbon (C) export from terrestrial ecosystems is a potentially important flux for the net catchment C balance and links the biogeochemical C cycling of terrestrial ecosystems to their downstream aquatic ecosystems. We have monitored hydrology and stream chemistry over 3 years in ten nested catchments (0.6–15.1 km2) with variable peatland cover (0%–22%) and groundwater influence in subarctic Sweden. Total waterborne C export, including dissolved and particulate organic carbon (DOC and POC) and dissolved inorganic carbon (DIC), ranged between 2.8 and 7.3 g m–2 year–1, representing ~10%–30% of catchment net ecosystem exchange of CO2. Several characteristics of catchment waterborne C export were affected by interacting effects of peatland cover and groundwater influence, including magnitude and timing, partitioning into DOC, POC, and DIC and chemical composition of the exported DOC. Waterborne C export was greater during the wetter years, equivalent to an average change in export of ~2 g m–2 year–1 per 100 mm of precipitation. Wetter years led to a greater relative increase in DIC export than DOC export due to an inferred relative shift in dominance from shallow organic flow pathways to groundwater sources. Indices of DOC composition (SUVA254 and a250/a365) indicated that DOC aromaticity and average molecular weight increased with catchment peatland cover and decreased with increased groundwater influence. Our results provide examples on how waterborne C export and DOC composition might be affected by climate change.