We tested the hypothesis that CO₂ supersaturation along the aquatic conduit over Sweden can be explained by processes other than aquatic respiration. A first generalized‐additive model (GAM) analysis evaluating the relationships between single water chemistry variables and pCO₂ in lakes and streams revealed that water chemistry variables typical for groundwater input, e.g., dissolved silicate (DSi) and Mg²⁺ had explanatory power similar to total organic carbon (TOC). Further GAM analyses on various lake size classes and stream orders corroborated the slightly higher explanatory power for DSi in lakes and Mg²⁺ for streams compared with TOC. Both DSi and TOC explained 22–46% of the pCO₂ variability in various lake classes (0.01–>100 km²) and Mg²⁺ and TOC explained 11–41% of the pCO₂ variability in the various stream orders. This suggests that aquatic pCO₂ has a strong groundwater signature. Terrestrial respiration is a significant source of the observed supersaturation and we may assume that both terrestrial respiration and aquatic respiration contributed equally to pCO₂ efflux. pCO₂ and TOC concentrations decreased with lake size suggesting that the longer water residence time allow greater equilibration of CO₂ with the atmosphere and in‐lake mineralization of TOC. For streams, we observed a decreasing trend in pCO₂ with stream orders between 3 and 6. We calculated the total CO₂ efflux from all Swedish lakes and streams to be 2.58 Tg C yr⁻¹. Our analyses also demonstrated that 0.70 Tg C yr⁻¹ are exported to the ocean by Swedish watersheds as HCO₃⁻ and CO₃²⁻ of which about 0.56 Tg C yr⁻¹ is also a residual from terrestrial respiration and constitute a long‐term sink for atmospheric CO₂. Taking all dissolved inorganic carbon (DIC) fluxes along the aquatic conduit into account will lower the estimated net ecosystem C exchange (NEE) by 2.02 Tg C yr⁻¹, which corresponds to 10% of the NEE in Sweden.