Acidic groundwater generated from acid sulphate soil (ASS) is a major geo-environmental problem in Australia. A permeable reactive barrier (PRB) with recycled concrete aggregates as the reactive material has received considerable attention as an innovative, cost effective technology for passive treatment of acidic groundwater in ASS terrain. Laboratory column experiments conducted at the University of Wollongong investigated the acid neutralisation behaviour of recycled concrete and its potential to remove dissolved aluminium (Al) and iron (Fe). The recycled concrete effectively treated the acidic groundwater, resulting in near-neutral effluent pH and complete removal of Al and Fe. However, armouring of the concrete by precipitated secondary Al- and Fe-bearing minerals reduced the acid neutralisation capacity of the concrete by ~50%. Hence, it is of utmost importance to analyse quantitatively the effect of armouring on the surface of the reactive material. This study assesses the reduction in hydraulic conductivity caused by secondary mineral precipitation in the treatment of acidic groundwater under two operating conditions: constant flow rate and constant head. The precipitated volumes of secondary minerals were obtained from stoichiometric calculations using measured changes in their aqueous concentrations. The Kozeny-Carman equation and Darcy’s Law were adopted to measure the hydraulic conductivity at different pore volumes. While the results revealed almost similar reductions in hydraulic conductivity with respect to time under both operating conditions, the hydraulic conductivity reduction under constant flow rate was faster than in the case of constant head.