Degradation of chlorinated ethenes (CEs) in low conductivity layers of aquifers reduces pollution plume tailing and accelerates natural attenuation timeframes. The degradation pathways involved are often different from those in the higher conductive layers and might go undetected when only highly conductive layers are targeted in site assessments. Reactive transport model simulations (PHT3D in FloPy) were executed to assess the performance of dual carbon and chlorine compound specific stable isotope analysis (CSIA) in degradation pathway identification and quantification in a coupled physical-chemical heterogeneous virtual aquifer. Degradation rate constants were assumed correlated to the hydraulic conductivity: positively for oxidative transformation (higher oxygen availability in coarser sands) and negatively for chemical reduction (higher content of reducing solids in finer sediments). Predicted carbon isotope ratios were highly heterogeneous. They generally increased downgradient of the pollution source but the large variation across depth illustrates that monotonously increasing isotope ratios downgradient, as were associated with the oxidative component, are not necessarily a common situation when degradation is favorable in low conductivity layers. Dual carbon-chlorine CSIA performed well in assessing the occurrence of the spatially separated degradation pathways and the overall degradation, provided appropriate enrichment factors were known and sufficiently different. However, pumping to obtain groundwater samples especially from longer well screens causes a bias towards overestimation of the contribution of oxidative transformation associated with the higher conductive zones. As degradation was less intense in these highly conductive zones under the simulated conditions, overall degradation was underestimated. In contrast, in the usual case of limited CSIA data, dual CSIA plots may rather indicate dominance of chemical reduction, while oxidative transformation could go unnoticed, despite being an equally important degradation pathway.