Despite rapid population aging and depopulation in Japan, groundwater nitrate contamination still poses serious environmental problems. One of the main factors contributing to elevated nitrate levels in Japanese groundwater sources is agricultural intensification, frequently because of increased fertilizer use. We investigated the impact of population aging and depopulation on groundwater nitrate contamination on a western Japanese island that has extensive citrus farming. In comparison to Ocho village, where the average age of farmers is 73 years, Kubi village’s farmers are slightly older on average, at 76 years, and agricultural land has decreased by 46% over the past ten years, from 2005 to 2015. Ocho had 830 residents, which was twice as many as Kubi. In comparison to Ocho (4.8 mg/L), Kubi village had higher average NO3−−N concentrations (6.6 mg/L). NO3−−N contamination sources in Kubi and Ocho were determined using stable nitrogen isotopes and a Bayesian isotope mixing model. These source distributions were more strongly associated with social and land use factors. It was believed that the older farmers in Kubi employed a significant quantity of chemical fertilizers, which caused inefficient nitrogen uptake by plants, leading to increased leaching and more groundwater contamination than in Ocho.