Our research addresses the challenge that bioclogging poses to the operation of Soil Aquifer Treatment (SAT) systems. A conceptual model that considers the dynamic interactions between microbial activity, water flow, and soil clogging is presented and studied to optimize SAT operation. Simulations show that tweaking wet and dry periods enhance water infiltration and SAT performance. Additionally, a link between the biomass spatial distribution and the wet and dry cycles was discovered.