A flow system is described that is based on sequential injection analysis (SIA) and is suitable for the fast determination of ammonia and phosphate in river and marine waters. It is applicable to nutrient mapping in inhomogeneous coastal areas like the Wadden Sea, and was optimised on several cruises on the North Sea. The high sample throughput of 120 samples per analyte per hour and the low reagent consumption (ammonia: 62.5 μL; phosphate: 60 μL) were achieved using a home made programme written in the python programming language. The determination of free reactive phosphate is based on the reaction of phosphate with acidic molybdate to phosphomolybdate which forms nonfluorescent ion pairs with rhodamine 6G. The remaining rhodamine fluorescence is detected at 550 nm with an excitation at 470 nm. Ammonia is determined with the help of o-phthaldialdehyde and sodium sulfite. At 85°C and a reaction time of at least one minute a fluorescent species (exc. 365nm, em. 425nm) is formed. The detection limits are (3σ) 0.3 μmol L ^-1 for phosphate and 1 μmol L ^-1 for ammonia.