Linking biogeochemical processes to water flow paths and solute travel times is important for understanding internal catchment functioning and control of water quality. Base cation weathering is a process closely linked to key factors affecting catchment functioning, including water pathways, soil contact time, and catchment characteristics, particularly in silicate-dominated areas. However, common process-based weathering models are often calibrated and applied for individual soil profiles, which can cause problems when trying to extrapolate results to catchment scale and assess consequences for stream water and groundwater quality. Therefore, in this work, base cation export was instead modelled using a fully calibrated 3D hydrological model (Mike SHE) of a boreal catchment, which was expanded by adding a relatively simple but still reasonably flexible and versatile weathering module including the base cations Na, K, Mg, and Ca. The results were evaluated using a comprehensive dataset of water chemistry from groundwater and stream water in 14 nested sub-catchments, representing different catchment sizes and catchment characteristics. The strongest correlations with annual and seasonal observations were found for Ca (r = 0.89-0.93, p < 0.05), Mg (r = 0.90-0.95, p < 0.05), and Na (r = 0.80-0.89, p < 0.05). These strong correlations suggest that catchment hydrology and landscape properties primarily control weathering rates and stream dynamics of these solutes. Furthermore, catchment export of Mg, Ca, and K was strongly connected to travel times of discharging stream water (r = 0.78-0.83). Conversely, increasing Na export was linked to a reduced areal proportion of mires (r = -0.79). The results suggest that a significant part (~45%) of the catchment stream export came from deep-soil weathering sources (>2.5 m). These results have implications for terrestrial and aquatic water quality assessments. If deep soils are present, focusing mainly on the shallow soil could lead to misrepresentation of base cation availability and the acidification sensitivity of groundwater and water recipients such as streams and lakes.