This paper describes a flow potentiometric method for determination of ammonium at low levels. A new diffusion cell coupled to an ammonium ion electrode was used as the potentiometric detector. This method eliminates interference to the ammonium ion electrode. When the stopped-flow method is employed for the acceptor stream, ammonium ions can be accumulated in the acceptor solution in the diffusion cell, giving high selectivity and sensitivity. The lower linear value of the proposed method can reach 1 × 10−6mol L−1with an accumulation time of 5 min. The method is simple, sensitive and suitable for online determination of ammonium in water samples. It has been applied to the determination of ammonium in rain water and river water, and recoveries of 95 – 104% were obtained. The relative standard deviation of seven replicate analyses for all samples was 1.1 – 2.7%.