Natural source zone depletion (NSZD) of light non-aqueous phase liquids (LNAPLs) may be a valid long-term management option at petroleum impacted sites. However, its future long-term reliability needs to be established. NSZD includes partitioning, biotic and abiotic degradation of LNAPL components plus multiphase fluid dynamics in the subsurface. Over time, LNAPL components are depleted and those partitioning to various phases change, as do those available for biodegradation. To accommodate these processes and predict trends and NSZD over decades to centuries, for the first time, we incorporated a multi-phase multi-component multi-microbe non-isothermal approach to representatively simulate NSZD at field scale. To validate the approach we successfully mimic data from the LNAPL release at the Bemidji site. We simulate the entire depth of saturated and unsaturated zones over the 27 years of post-release measurements. The study progresses the idea of creating a generic digital twin of NSZD processes and future trends. Outcomes show the feasibility and affordability of such detailed computational approaches to improve decision-making for site management and restoration strategies. The study provided a basis to progress a computational digital twin for complex subsurface systems.