Generation of acidic groundwater attributed to pyrite oxidation in low-lying acid sulfate soil causes substantial damage to the soil-water environment and civil infrastructure. The installation of Permeable Reactive Barrier (PRB) is a frontier technology in the field of acid neutralisation and for removing toxic heavy metal cations, e.g. soluble Fe and Al. This study aims to assess the potential of limestone (calcite) aggregates as the PRB's main reactive material in low-lying pyritic land. During long-term laboratory column experiments, a significant capacity of limestone for removing the contaminant chemical species was observed. Nevertheless, the formation of secondary mineral precipitates upon geochemical reactivity within the granular media in the PRB caused armouring and chemical clogging that diminished the rate of reactivity, i.e. the treatment capacity of calcite aggregates, mainly at the entrance zone of the porous media. Flow properties were altered due to blockage of pores; for instance, hydraulic conductivity was reduced by 25% at the inlet zone. Non-homogeneous clogging towards the outlet was analysed, and the time-dependent effect on longevity of a limestone column was studied and quantified.