A Semi- automated flow injection analysis (FIA) unit was build-up for determination of ammonium ion in water samples from the Shatt Al-Arab River during the period from October 2009 to September 2010. The ammonium concentrations in water have been measured, at each of the eight stations (Qurnah (Tigres), Qurnah (Euphrates), Saad Bridge, Garmat Ali, Ashar, Abu Al-Khaseeb, Al-Seeba and Fao), monthly. The results indicated that (NH4+) concentrations increasing during May, June and July, 2010 especially in stations 5 and 6 were 0.95, 1.35 µg/ml , 1.30, 1.25 µg/ml and 1.45, 1.40 µg/ml, respectively. The FIA unit was applied successfully for the determination of ammonium in Shatt Al-Arab water sample and provide simple, fast, and reproducible methods for ammonium determination in water.