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 During the recent decades، the increasing trends in nitrate ion concentration in ground water sources have meant more research to find effective procedures for the prevention of even more water contamination by nitrogen sources. In this study a pilot was designed to examine the application of biological method for eliminating nitrate from the water of well No.903 of Mehrabad Airport، Tehran، Iran. Design، installation and running processes were done from April to November 2003. A fixed biological bed containing five-centimeter trunk pipes 16 mm in diameter were installed in the reactor and the system was operated with upflow current. Instead of Methanol، Acetic acid was used as the carbon source because of its easier acceptance by the public، lower price and availability as well as easier storage. The pilot was run in different hydraulic retention times from 48 h up to one hour. Considering economical، operational and maintenance factors، retention time of 2 h was determined to be optimum، in which 77% nitrate removal was achieved. Considering a ratio of 2 for COD/N، inlet COD of about 140 mg/L and the optimum retention time، COD removal of about 80% is also accomplished in this process. The amount of nitrite concentration، pH values، COD and turbidity is also evaluated versus different hydraulic retention times.