Groundwater and river water are essential in geochemical transportation from land to sea. Freshwater discharge to the coastal sea as groundwater sometimes has large geochemical fluxes comparable to river water; however, it is more challenging to monitor groundwater than river water. In this study, we assessed the carbon cycle including an underground system in a highly porous coastal area along Mt. Chokai, northern Japan, where abundant submarine spring water emerges. Groundwater and river water chemistries are generally characterized by silicate weathering, reflecting the andesitic lava that occupies the basin. Groundwater discharge was determined using mass balance calculations, including precipitation, river water discharge, and evapotranspiration. Considering the underground dissolved bicarbonate flux from land to ocean, the CO2 consumption by silicate weathering in the western foothills of Mt. Chokai is calculated to be 8.8 ± 0.15 t-C/km2/yr, which is significantly larger than the case where only river water flux was evaluated (4.7 ± 0.25 t-C/km2/yr). Therefore, considering underground flux when estimating the amount of chemical weathering in coastal watersheds is crucial.