A study was conducted to evaluate long-term trends in nitrate concentrations and to try to identify the origin of nitrate using stable isotopes (¹⁵N_NO3⁻ and ¹⁸O_NO3⁻) in the aquifers of the western Central Valley, Costa Rica, where more than 1 million people depend on groundwater to satisfy their daily needs. Data from 20 sites periodically sampled for 4 to 17 years indicate an increasing trend in nitrate concentrations at five sites, which in a period ranging from 10 to 40 years, will exceed recommended maximum concentrations. Results of isotopic analysis indicate a correspondence between land use patterns and the isotopic signature of nitrate in groundwater and suggest that urbanization processes without adequate waste disposal systems, followed by coffee fertilization practices, are threatening water quality in the region. We conclude that groundwater management in this area is not sustainable, and that land use substitution processes from agricultural activity to residential occupation that do not have proper sewage disposal systems may cause a significant increment in the nitrate contaminant load.