A sequential injection system for phosphate determination within a wide concentration range was developed for water samples with high salinity levels. The determination is based on molybdenum blue chemistry using the standard addition quantification method. The detection system included a multi-reflective flow cell coupled to a light emitting diode, enabling the minimization of the schlieren effect. The developed system gave a LOD of 0.3 μmol P L−1 and LOQ of 1.1 μmol P L−1 with a sample consumption of 125 μL. A determination rate of about 30 h−1 was obtained, and the developed method was effectively applied to interstitial, transitional and coastal waters.