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 δ15NNH4 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 δ15NNH4 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 E. coli 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.