Accurate and automated determination methods for silicate and phosphate are in high demand to improve understanding of biogeochemistry and ecology in dynamic and complex estuarine-coastal ecosystems. Here, a portable automated analyzer is reported for the simultaneous determination of silicate and phosphate in water samples with varying salinity. After comprehensive optimization of the chemical reactions and flow manifold, the system demonstrated limits of detection of 0.09 and 0.05 μmol L−1 for silicate and phosphate, respectively, exhibiting linearity at concentrations up to 400 and 200 μmol L−1 with automated dilution, achieving relative standard deviations (n = 11) of 0.27% (20 μmol L−1 silicate), 0.51% (5 μmol L−1 phosphate) and 0.80% (1 μmol L−1 phosphate). Compared with similar automated flow analyzers, the system exhibited advantages, such as low consumption of reagents (10–20 μL/sample), portability (4.8 kg), rapid start-up (5 min), reliability (automated analysis of quality control sample) and applicability within a broad salinity range (from 0 to 35) allowing analysis of dynamic estuarine and seawater samples. The system was successfully applied to a routine monitoring program by a national marine station and is potentially suitable for installation on different observation platforms for on-line and real-time underway analysis of nutrients in coastal areas.