Water table fluctuations play a significant role in the redistribution of chemical species, microorganisms and organic pollutants in aquifers by creating favorable zones for reactive processes. This in turn is expected to affect the extent and pathways of biodegradation of halogenated contaminants such as dichloromethane (DCM). Here, a multi-phase flow reactive transport model (RTM) was developed to identify the main drivers of DCM biodegradation in aquifers under steady-state and transient conditions. The RTM includes a description of multi-phase flow, redox conditions, four characteristic bacterial populations and stable isotopologues (i.e., 13C/12C and 37Cl/35Cl) of DCM according to pathway-specific reactions. Dissolved organic carbon (DOC) was also included as a carbon source for non-DCM degrading populations yielding a more realistic heterotrophic groundwater microbial community. Numerical simulations of eight model scenarios were compared with experimental results from laboratory aquifers. Key biogeochemical processes involved in DCM biodegradation were captured, particularly across the capillary fringe. Only model scenarios of DCM degradation by multiple bacterial metabolisms were able to reproduce the dynamics observed in the laboratory aquifers. The observed and computed enrichment of 13C and 37Cl isotopes over time confirmed enhanced DCM biodegradation during water table fluctuations and highlighted interactions between different bacterial metabolisms. In particular, our RTM suggested that heterotrophic groundwater bacteria played a key role in regulating O2-depletion and redox conditions across fluctuation zones during parallel DOC mineralization. The produced CO2 favored metabolic activity of anaerobic DCM degraders requiring CO2 for their specific fermentative pathways. This study underscores the added value of integrating multi-phase flow, stable isotopes and distinct bacterial populations to understand natural attenuation of DCM in contaminated groundwater.