An autonomous microfluidic sensor for phosphate in environmental waters has been developed and assessed in laboratory and field trials. The sensor is based on the molybdenum yellow method for phosphate detection in which a phosphate-containing sample is mixed with a reagent containing ammonium molybdate and ammonium metavanadate in an acidic medium. The yellow-colored compound which is formed absorbs strongly below 400nm and its absorbance is proportional to the concentration of phosphate in the original sample. The sensor utilizes a microfluidic manifold where mixing, reaction and detection take place. Optical detection is performed using a LED (light emitting diode) light source and a photodiode detector. The sensor also combines pumping system, power supply, reagent and waste storage, and wireless communications into a compact and portable device. Here we report the successful use of the sensor to monitor phosphate levels in an estuarine environment.