This reactive transport modeling study presents a follow up to the mass balance-based identification and quantification of the main hydrogeochemical processes that occurred during an aquifer storage and recovery (ASR) trial in an anoxic sandy aquifer (Herten, the Netherlands). Kinetic rate expressions were used to simulate oxidation of pyrite, soil organic matter (SOM), and ferrous iron, and dissolution of calcite and Mn-siderite. Cation exchange, precipitation of Fe- and Mn-(hydr)oxides, and surface complexation were treated as equilibrium processes. The PHREEQC model was automatically calibrated with PEST to observations from the first ASR cycle, and was then allowed to run for all 14 cycles to evaluate its long term performance. A sensitivity analysis was conducted to find the most controlling model parameters. Pyrite was ranked as the most important reductant, followed by SOM, whereas Fe(II) was least important. Moreover, the pH and oxygen gradients were found to enhance the rate of pyrite over SOM oxidation with distance away from the ASR well. The increasing sorption capacity of precipitating Fe-hydroxides was reflected by the decreasing Fe(II) concentrations with subsequent cycles whereas Mn(II) showed a tendency to mobilize during recovery and remain above standards. Oxidation and dissolution rates were found to depend on travel time and injection rate as well as on the presence or absence of flow. Oxygen enrichment of the injection water increased oxidation rates and therefore accelerated the aquifer’s leaching from its reactive species. We specifically focused on impeding the release of Mn(II) to the groundwater, a process that acted as a restraining factor for the feasibility of ASR application at this site. The undesirable side-effects of oxygen enrichment as well as the Mn(II) issues were found to be partly suppressed by enriching the source water with pH buffers according to scenario simulations.