The groundwater flow systems and chemistry in the deep part of the coastal area of Japan have attracted attention over recent decades due to government projects such as geological disposal of radioactive waste. However, the continuous groundwater flow system moving from the shallow to deep parts of the sedimentary soft rock has not yet been characterized. Therefore, the Cl^–, δD and δ¹⁸O values of the pore water in the Horonobe coastal area in Hokkaido, Japan, were measured to 1,000 m below the ground surface, and a vertical profile of the pore-water chemistry was constructed to assist in elucidating groundwater circulation patterns in the coastal area. The results show that the groundwater flow regime may be divided into five categories based on groundwater age and origin: (1) fresh groundwater recharged by modern rainwater, (2) fresh groundwater recharged by paleo rainwater during the last glacial age, (3) low-salinity groundwater recharged during the last interglacial period, (4) mixed water in a diffusion zone, and (5) connate water consisting of paleo seawater. These results suggest that the appearance of hydrological units is not controlled by the boundaries of geological formations and that paleo seawater is stored in younger Quaternary sediments.