A sensitive reagent-injection flow analysis method for the spectrophotometric determination of nitrate in marine, estuarine and fresh water samples is described. The method is based on the reduction of nitrate in a micro column containing zinc granules at pH 6.5. The nitrite formed is reacted with sulfanilamide and N-(1-naphthyl)ethylene diamine (Griess reagent), and the resulting azo compound is quantified spectrophotometrically at 520 nm. Water samples in the range of 3a??700 I?g La??1 NO3a??a??N can be processed with a throughput of up to 40 samples per hour, a detection limit of 1.3 I?g La??1 and reproducibility of 1.2 RSD (50 I?g La??1 NO3a??a??N, n = 10). The proposed method was successfully applied for the determination of nitrate in estuarine waters and the reliability was assessed by the analyses of certified reference materials and recovery experiments. The method is suitable for waters with a wide range of salinities, and was successfully used for more than 3200 underway nitrate measurements aboard SV Pelican1 in the a??Two Baysa?? cruise in January 2010.