We report a high performance autonomous analytical system based on the vanadomolybdate method for the determination of soluble reactive phosphorus in seawater. The system combines a microfluidic chip manufactured from tinted poly (methyl methacrylate) (PMMA), a custom made syringe pump, embedded control electronics and on-board calibration standards. This “lab-on-a-chip” analytical system was successfully deployed and cross-compared with reference analytical methods in coastal (south west England) and open ocean waters (tropical North Atlantic). The results of the miniaturized system compared well with a reference bench-operated phosphate auto-analyser and showed no significant differences in the analytical results (student’s t-test at 95% confidence level). The optical technology used, comprising of tinted PMMA and polished fluidic channels, has allowed an improvement of two orders of magnitude of the limit of detection (52nM) compared to currently available portable systems based on this method. The system has a wide linear dynamic range 0.1–60μM, and a good precision (13.6% at 0.4μM, n=4). The analytical results were corrected for silicate interferences at 0.7μM, and the measurement frequency was configurable with a sampling throughput of up to 20 samples per hour. This portable micro-analytical system has a low reagent requirement (340μL per sample) and power consumption (756J per sample), and has allowed accurate high resolution measurements of soluble reactive phosphorus in seawater. •Automated analytical “Lab-on-a-chip” system for phosphate determination.•Microfluidic analyser with reduced power and reagent consumption.•Successful field test and comparison with reference methods.•Correction of results for silicate interference.