Managed aquifer recharge is an increasingly popular technique to secure and enhance water supplies. Among a range of recharging techniques, single‐well aquifer storage and recovery (ASR) is becoming a common option to either augment drinking water supplies or facilitate reuse of reclaimed water. For the present study a conceptual biogeochemical model for reclaimed water ASR was developed and incorporated into an existing reactive multicomponent transport model. The conceptual and numerical model for carbon cycling includes various forms of organic and inorganic carbon and several reactive processes that transfer carbon within and across different phases. The major geochemical processes considered in the model were microbially mediated redox reactions, driven by the mineralization of organic carbon, mineral dissolution/precipitation, and ion exchange. The numerical model was tested and applied for the analysis of observed data collected during an ASR field experiment at Bolivar, South Australia. The model simulation of this experiment provides a consistent interpretation of the observed hydrochemical changes. The results suggest that during the storage phase, dynamic changes in bacterial mass have a significant influence on the local geochemistry in the vicinity of the injection/extraction well. Farther away from the injection/extraction well, breakthrough of cations is shown to be strongly affected by exchange reactions and, in the case of calcium, by calcite dissolution.