The numerous water bodies and their riparian zones in the boreal zone are crucial to lateral carbon transport and can thus be very significant for carbon cycle on the landscape level. Therefore, we installed automatic measurement systems with Vaisala CARBOCAP CO2 probes (Vaisala Oyj, Vantaa, Finland) in the riparian zone soil matrix around a small headwater lake, in the lake itself, and in the outflowing brook and followed the seasonal and diurnal variation in CO2 concentration as well as rain event-driven changes in this natural-state soil–lake–brook continuum in Southern Finland. Seasonal variation was greatest and concentrations highest deep in the soil and in the lake, but were also noticeable in the brook. On the other hand, diurnal variation was highest in shallow soil layers and the lake surface. In the brook, the influence of the riparian zone superseded that of the lake at less than 150 m distance, which resulted in wider variation and higher concentrations of CO2. After the rain event, the normal diurnal pattern was changed, and the CO2 concentration in the soil increased as water filled the soil pores and slowed down the diffusion. Even though the water with lower CO2 concentration from the lake diluted the CO2 concentration in the brook, the input from the soil dominated the flow after the rain and concentrations increased. On an annual basis, the flow of terrestrial dissolved inorganic carbon (DIC) into the aquatic ecosystem was 1–13% of terrestrial net ecosystem production (NEP).