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The origin of ammonium-nitrogen in Indonesian coastal groundwater has not been intensively examined, meanwhile the elevated concentration remains a concern. This research aims at tracing the potential sources of ammonium-nitrogen in the groundwater of Indramayu, Indonesia where groundwater is vital for livelihood. From results, a combined examination of nitrogen isotope, coliform bacteria, land-use, and geology confirmed the natural and anthropogenic origins of ammonium-nitrogen in the groundwater. In the brackish-water aquaculture region, groundwater has δ¹⁵N_NH4 values from +1.8 to +4.8‰ signifying that ammonium-nitrogen is derived from mineralization of organic nitrogen to ammonium. Furthermore, ammonium has a significantly positive relationship with sodium indicating the exchangeable ammonium is mobilized to groundwater via cation exchange. Meanwhile ammonium-nitrogen from anthropogenic waste was detected in agricultural and residential region. The groundwater has more varied δ¹⁵N_NH4 values, from −2.9 to +16.1‰, which implies attenuation of ammonium-nitrogen from several sources namely manure, mineral fertilizer, sewage, and pit latrines. Also, the presence of <i>E. coli</i> confirms the indication of human and animal waste contamination. However, since ammonium has no relationship with sodium, cation exchange is not feasible and ammonium-nitrogen flows into the groundwater from anthropogenic sources along with liquid wastes.