In an enhanced biological phosphorus reactor (EBPR), most poly-phosphate accumulating microorganisms (PAOs) exist as microbial aggregates, or flocs. Information contributing to a better understanding of the internal structure and function of flocs can lead to improvements in the modeling, design and operation of EBPR systems in wastewater treatment. A phosphate ion-selective microelectrode has been developed and was used to measure the phosphate profiles in flocs. The microelectrode uses cobalt as the sensing material and shows very good selectivity towards orthophosphate ions (H2PO4(-), HPO4(2-) and PO4(3-)). The potentiometric response showed a linear relationship with the logarithm of phosphate concentrations, with a slope of 31.5 mV per decade change of concentration. The solution pH did not show a significant effect on the microelectrode performance within the pH range of 7.5 to approximately 8.0. The effect of ionic strength was also investigated. Measurements using this microelectrode were made on activated sludge floc samples taken from a municipal wastewater treatment plant.