Major ion chemistry, oxygen isotope and multivariate statistical method were used to investigate aquifers interaction in the southwestern foot of Mt. Fuji, the largest Quaternary stratovolcano in Japan. Groundwater samples were taken from different aquifers which are in descending order: the superficial aquifer, aquifers residing in the New Fuji Lava and the Old Fuji Aquifer. The geochemical signatures of groundwaters, notably the molar Na/Cl and Na/Ca ratios, oxygen stable isotope and the nitrate contents evolution, in conjunction with the hierarchical cluster analysis allowed to highlight three groundwater systems differing by their hydrochemical facies and residence time: 1) The shallow and highly polluted groundwaters of the superficial aquifer, 2) Groundwaters of the New Fuji Lava moderately mineralized and polluted, 3) The non-polluted groundwaters of the Old Fuji Aquifer. Waters of these systems are interacting. In fact, nitrate contamination, in provenance from the superficial aquifer, was detected in the New Fuji Lava layers and the deep groundwaters of the Old Fuji. Furthermore, many samples taken from the Old Fuji Aquifer were characterized by a relatively enriched δ¹⁸O. These results prove that groundwaters of the New Fuji layers could be mixed with groundwaters of the overlaying superficial aquifer and that these groundwaters, supposed to flow only horizontally, can flow vertically through the cracks, causing the mixing of deep and old groundwater of the Old Fuji with groundwaters recently recharged and polluted.