This study focuses on coupling geochemistry with geo-hydraulics to enable time-dependent modelling of the remediation of acidic groundwater using an alkaline permeable reactive barrier (PRB). Chemical clogging due to secondary mineral precipitates reduces the porosity and hydraulic conductivity of the reactive medium. The governing equations are incorporated into commercial numerical codes, MODFLOW and RT3D. An original algorithm was developed for RT3D to simulate geochemical reactions occurring in the PRB. The results and the model predictions are in agreement, confirming that the hydraulic conductivity reduction due to mineral precipitation occurs at the start of permeation and continues until halfway through the testing phase.