AbstractGroundwater is an essential resource providing water for societies and sustaining surface waters. Although groundwater at intermediate depth could be highly influential at regulating lake and river surface water chemistry, studies quantifying organic and inorganic carbon (C) species in intermediate depth groundwater are still rare. Here, we quantified dissolved and gaseous C species in the groundwater of a boreal catchment at 3‐ to 20‐m depth. We found that the partial pressure of carbon dioxide (pCO2), the stable carbon isotopic composition of dissolved inorganic carbon (δ13C‐DIC), and pH showed a dependency with depth. Along the depth profile, a negative relationship was observed between pCO2 and δ13C‐DIC and between pCO2 and pH. We attribute the negative pCO2‐pH relationship along the depth gradient to increased silicate weathering and decreased soil respiration. Silicate weathering consumes carbon dioxide (CO2) and release base cations, leading to increased pH and decreased pCO2. We observed a positive relationship between δ13C‐DIC and depth, potentially due to diffusion‐related fractionation in addition to isotopic discrimination during soil respiration. Soil CO2 may diffuse downward, resulting in a fractionation of the δ13C‐DIC. Additionally, the dissolved organic carbon at greater depth may be recalcitrant consisting of old degraded material with a greater fraction of the heavier C isotope. Our study provides increased knowledge about the C biogeochemistry of groundwater at intermediate depth, which is important since these waters likely contribute to the widespread CO2 oversaturation in boreal surface waters.