Reactive transport models (RTMs) are widely adopted supporting tools for the design and management of aquifer in-situ bioremediation systems. However, their use has not been yet fully demonstrated for the design and management of operational-scale sequential bioremediation system (SBSs). In this work, a multispecies RTM was developed to reproduce an SBS coupled to a pump-and-treat (P&T) system in a chloroethene-polluted alluvial aquifer of Northern Italy. It is one of the first-ever documented applications of multispecies process-based RTM to simulate an operational-scale SBS. Two different model configurations were created to study the importance of adopting a more homogeneous or heterogeneous spatial distribution of transport parameters. The first configuration embedded three different reaction zones (RZs), each one described by spatially—invariant first-order reaction rates (\(k\)) simulating parent-daughter transformation of chloroethenes (PCE→TCE→DCE→VC). The second configuration embedded a spatially variant distribution of reaction rates within the three RZs, resulting in a more heterogeneous parametrization. Given the larger number of fitting parameters, the more heterogeneous model provided a better match of the field observations. Compared to it, calibrated \(k\) obtained from the more homogeneous model were largely underestimated for more-chlorinated compounds (PCE, TCE) and overestimated for less-chlorinated compounds (DCE, VC). The heterogeneous model showed that the capacity of the SBS to degrade the chemicals varied significantly across the different site areas, a feature not captured by the homogeneous model, and which could have important implications regarding the potential closure of selected P&T wells.