A sequential injection analysis system (SIA) is described which is suited for the fast determination of filterable molybdate reactive phosphate (FRP, 0.2 μm) in coastal waters. It processes up to 270 samples per hour with a detection limit (3σ) of 0.05 μM and is used for surface mapping of phosphate in areas with steep concentration gradients like the Wadden Sea. The determination is based on the reaction of phosphate with acidic molybdate to phosphomolybdate, which builds non-fluorescent ion pairs with rhodamine 6G. The remaining rhodamine fluorescence is detected at 550 nm with an excitation at 470 nm. Syringe pump, valve and detector were controlled by a self made python programme, which was optimised for high speed SIA measurements in monitoring applications.