Aquifer depositional environments in Quaternary and Neogene (Koetoi) formations in Horonobe district, Hokkaido, were evaluated from the C/S ratio and boron content, and the organic matter sources were characterized by the C/N and C/Br ratios. Groundwater samples were also analyzed for the C/N and C/Br ratios and lignin concentrations. Although the C/N and C/Br ratios in the sediments varied in harmony with their marine or terrestrial depositional environments, the C/N ratios in some marine Quaternary sediments were as high as those in terrestrial Quaternary sediments. Groundwater in Quaternary marine formations showed high lignin concentrations and C/N ratios when the sediments were heavily contaminated with terrestrial organic matter. This suggests a strong correlation between the organic matter sources in the sediments and the organic composition of the associated groundwater. However, groundwater in the Koetoi formation showed high concentrations of nitrogen-containing organic matter, indicating accumulation of these substances through prolonged diagenesis.