The main objective of this study is the establishment of innovative purification systems through the conceptualisation of reactive barriers in soil for artificial recharge of groundwater with treated wastewater. Numerical integration of hydrodynamics and biogeochemical processes controlling the effectiveness of this engineering system is applied to design soil column experiments. This leads to the elaboration of a combined aerobic/anaerobic environment to ensure the successive nitrification of rich ammonium wastewater and the denitrification mechanisms reducing NO3– according to heterotrophic denitrification and pyrite oxidation. A MIN3P reactive flow and transport model is used to reproduce an experimental flow-through column. Calculated concentrations of CH2O and NO3− are consistent with experimental results. Agreement between model and experimental results makes it possible to understand major processes taking place in the column and optimises future treatment experiments.