In coastal Australia, shallow pyrite deposits (FeS2) in low-lying terrains oxidise to produce sulfuric acid that pollutes the soil and groundwater, thus adversely affecting the environment, coastal development, fisheries, and agricultural development. Permeable Reactive Barrier (PRB), an underground granular filter, is a practical engineering technique that neutralises groundwater acidity. Two pilot-scale PRBs were installed in the lower Shoalhaven floodplain, NSW, Australia, to treat the acidic water using alkaline aggregates as the reactive material. However, during the treatment of contaminated groundwater, the entrapment of biomass generated by bacteria and secondary mineral precipitates within the granular matrix reduces the hydraulic conductivity and porosity of the PRB and affects its longevity. Real-time monitoring data of the field PRB and its clogging patterns along the centreline of the PRB are discussed in this paper. Clogging and armouring were non-homogeneous along the flow path, and the acid neutralisation capacity at the inlet of the PRB decreased by 31% in 15 years due to clogging, but only a 6% reduction was observed at the outlet.