To elucidate geochemical characteristics of groundwater and sources of dissolved ions in groundwater at the southern slope and the base of Mt. Fuji, central Japan, in 2011 and 2012, dissolved ions in 199 samples of both well water or spring water from the study region and 12 monthly precipitation samples at each of four elevations were collected and analyzed. Most of the groundwater was of the Ca-HCO3 type. The study region was divided from the near summit to the base of the mountain into four areas based on water quality, topography, geology, and land use at the watershed. The concentration of chlorine ion (Cl−) in the groundwater and precipitation tended to decrease with elevation, and the Na+/Cl− ratio in the precipitation (0.56 on average) was close to that of seawater (0.56) at all sites. The atmosphere-derived fractions of major cations in the groundwater, which were estimated by assuming that all Cl− was derived from sea salt in the atmosphere, were in ascending order: Ca (average 0.05), Mg (0.08), K (0.28), and Na (0.29). The concentrations of PO43− and F− and the cation: Cl− ratios of all cations were high in the groundwater in the eastern area, where the surface geology consists of Gotemba mud flow sediments, which are composed of volcanic materials of the Old Fuji period. These results indicate that groundwater quality is strongly affected by the basaltic materials composing Mt. Fuji, which are enriched with Ca and Mg, and are susceptible to chemical weathering, but differs between aquifers in volcanic rocks of the Old Fuji period (about 100 ka) and those in rocks of the New Fuji period (after about 10 ka). In the southwestern and southeastern areas, the groundwater was characterized by a high concentration of NO3−. Because tea plantations are distributed at upper elevations in these areas, we inferred the major source of nitrogen in the water to be fertilizer. Moreover, spring water was enriched more with NO3− than well water collected at similar elevations, suggesting that the recharge area of well water is at a higher elevation than the spring water recharge area.