The status of nitrate (NO3-), nitrite (NO2-) and ammonium (NH4 +) contamination in the water systems, and the mechanisms controlling their sources, pathways, and distributions were investigated for the Southeast Asian cities of Metro Manila, Bangkok, and Jakarta. GIS-based monitoring and dual isotope approach (nitrate delta15N and delta18O) suggested that human waste via severe sewer leakage was the major source of nutrient contaminants in Metro Manila and Jakarta urban areas. Furthermore, the characteristics of the nutrient contamination differed depending on the agricultural land use pattern in the suburban areas: high nitrate contamination was observed in Jakarta (dry fields), and relatively lower nutrients consisting mainly of ammonium were detected in Bangkok (paddy fields). The exponential increase in NO3--delta15N along with the NO3- reduction and clear delta18O/delta15N slopes of NO3- (approximately 0.5) indicated the occurrence of denitrification. An anoxic subsurface system associated with the natural geological setting (e.g., the old tidal plain at Bangkok) and artificial pavement coverage served to buffer NO3- contamination via active denitrification and reduced nitrification. Our results showed that NO3- and NH4+ contamination of the aquifers in Metro Manila, Bangkok, and Jakarta was not excessive, suggesting low risk of drinking groundwater to human health, at present. However, the increased nitrogen load and increased per capita gross domestic product (GDP) in these developing cities may increase this contamination in the very near future. Continuous monitoring and management of the groundwater system is needed to minimize groundwater pollution in these areas, and this information should be shared among adjacent countries with similar geographic and cultural settings.