A multi-commuted flow system coupled to a gas diffusion device was developed for the spectrophotometric determination of ammonium nitrogen in sea and estuarine waters. The efficiency of complexing agents to prevent precipitation of metallic hydroxides, due to the high pH value of the carrier solution, was studied. Under the optimised conditions, no interference was observed from different expected interfering ions as well as volatile amines. The proposed method provided the determination of NH4+ in concentrations ranging from 50 to 1000 μg L-1, with detection and quantification limits of 18 and 35 μg L-1, respectively. A determination rate of 20 h-1 was achieved, with good repeatability for 10 consecutive injections of sea and estuarine samples (relative standard deviations lower than 2.0%). Accuracy of the methodology was assessed through recovery assays in 10 samples and also by analysis of certified reference material.