Twenty-nine well waters obtained from the urban district of the northern Kyoto Basin were analyzed to determine four physical and two chemical parameters, and seven major and one minor components. Correlations among the major components suggest that they were generally originated from aerosol and soil. Shallow groundwater in the urban area was polluted with nitrate mainly because of the infiltration of surface water. Based on the geochemical characteristics, such as total ion concentrations, the concentrations of chloride and nitrate, geological settings of the wells, and compositional differences in major ions, the twenty-nine well waters were classified into four categories, i.e., anthropogenically contaminated waters in the urban area, deep well waters in the urban area, waters in the hilly area, and waters in the suburb areas. Two paths of groundwater flow toward the south in the urban area were inferred, judging from the similarity in water chemistry elucidated through concentration correlation matrix and pattern recognition methods. One of the flowing paths runs along the Kamo River and the other runs in the west of the previous path. The groundwaters flowing through the two paths would be mixed in an underlying thick gravel stratum.