In this work, a numerical model was developed with the aim to study the effect of drying period (DP) duration on the biogeochemical state of a soil aquifer treatment (SAT) system, and to enhance its functionality accordingly. The model was calibrated and verified using data series from long-column experiments, and sensitivity analysis was performed. Considering unsaturated water flow, air movement, solute transport, and the main microbial-mediated kinetic reactions relevant to SAT, we examined outflow quality and reaction rates in response to seven DP durations while the flooding period (FP) durations were kept constant. The results show that extension of the aerobically active region occurs in response to longer DPs and suggest that very long DPs (>3 times the FPs) may not pose further advantage compared with medium-length DPs (2.5–3 times the flooding periods). A simple optimization process was demonstrated for the experimental SAT system presented, considering outflow quality vs. infiltrated volume. An optimum was obtained at DP/FP ratio of ∼2.8. Although these results are system specific, similar biogeochemical models may be modified and used for hydraulic operation optimization in other SAT sites.