In many cases in Romania, the mineral waters (in the Neogene Volcanic area of the Eastern Carpathians), especially the carbonate waters, have ammonium in concentration over 0.5 mg/l. The main issue regarding the presence of ammonium is identifying if the concentration is due to the anthropogenic pollution or it is of endogenic origin. The geological, hydrogeological and hydrochemical data analysis resulted in a conceptual model of the aquifer’s spatial position, groundwater movement and mineralization, and ammonium occurrence. The geological and tectonic aspects, aquifer’s recharging, groundwater flow direction, absence of surface pollution sources and correlation of hydrochemical data, all indicate the underground origin of ammonium. The aquifer is generated in pliocene - quaternary granular deposits. In the basement of these granular deposits, in the fracture areas, the groundwater is mixed with carbon dioxide and ammonium emissions, produced in the volcanic chambers. The surface data correlation and the hydrochemical data analysis resulted in the confirmation of the deep ammonium origin. After groundwater flow modeling and ammonium transport simulation, the ammonium plume size and preferential transport directions have been finally elucidated.