Acidic groundwater generation from acid sulfate soil is a severe environmental and socio-economic problem in coastal Australia. A novel permeable reactive barrier (PRB) utilising recycled concrete aggregates as the reactive media was installed in the Shoalhaven Floodplain, south of Wollongong in Australia. The performance of the PRB has been monitored to study the acid neutralisation behaviour of recycled concrete and its potential to remove high concentrations of Al and Fe, which are threatening to living habitat. This study aims to couple geochemistry with geo-hydraulics in the remediation of acidic groundwater generated in acid sulfate soil terrain, which has not been addressed in the past (especially using recycled concrete aggregates), in view of time-dependent modelling and performance verification. Coupling includes complex geochemical reaction kinetics with transient groundwater flows. Moreover, chemical clogging due to mineral precipitates has rarely been quantified. Deposition of precipitated minerals in void spaces within the PRB reduces the porosity and hydraulic conductivity of the reactive medium, which in turn effects the reorientation of flow paths and changes in reaction times. The commercial numerical codes, MODFLOW and RT3D were used to couple the groundwater flow with reaction kinetics. A systematic algorithm was developed for RT3D to simulate geochemical reactions occurring in the PRB. The field results show good agreement with the model predictions. The hydraulic conductivity reductions occur near the entrance of the PRB due to the high amount of mineral precipitation. Compared to the entrance, hydraulic conductivity reductions were negligible midway and at the effluent end of the PRB.