The development and evaluation of a portable flow analysis system for the in situ determination of total phosphorus is described. The system has been designed with rapid underway monitoring in mind. The system employs an ultra-violet photo-reactor and thermal heating for peroxodisulfate digestion of total phosphorus to orthophosphate, followed by spectrophotometric detection with a multi-reflective flow cell and low-power light emitting diode using the molybdenum blue method. Reagents are stored under gas pressure and delivered using software controlled miniature solenoid valves. The fully automated system has a throughput of 115 measurements per hour, a detection limit of 1 i??g P L-1, and gives a linear response over the calibration range of 0i??200 i??g P L-1 (r2 = 0.9998), with a precision of 4.6 RSD at 100 i??g P L-1 (n = 10). Field validation of the instrument and method was performed in Port Philip and Western Port Bays in Victoria, SE Australia, where 2499 analyses were performed over a 25 h period, over a cruise path of 285 km. Good agreement was observed between determinations of samples taken manually and analysed in the laboratory and those measured in situ with the flow analysis system.