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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 δ¹⁵N and δ¹⁸O) 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⁻–δ¹⁵N along with the NO₃⁻ reduction and clear δ¹⁸O/δ¹⁵N slopes of NO₃⁻ (∼0.5) indicated the …