An automatable flow system for the continuous and long term monitoring of phosphate level has been developed using an amperometric detection method based on the use of a miniaturized sensor. This method is based on the monitoring of an electroactive complex obtained by the reaction between phosphate and a molybdate that is consequently reduced at the electrode surface. The use of a screen-printed electrode modified with carbon black nanoparticles (CBNPs) leads to the quantification of the complex at low potential, since CBNPs are capable to electrocatalitically enhance the phosphomolybdate complex reduction at +125 mV vs. Ag/AgCl without fouling problems. The developed system also incorporates reagents and waste storage, and is connected to a portable potentiostat for rapid detection and quantification of phosphate. Main analytical parameters as working potential, reagent concentration, type of cell and flow rate, were evaluated and optimized. This system was characterized by a low detection limit (6 µM). Interference studies were carried out. Good recovery percentages comprised between 89% and 131.5% were achieved in different water sources highlighting its suitability for field measurements.