The application of compound-specific stable isotope analysis (CSIA) was evaluated to characterise a complex groundwater contamination. For this purpose, δ13C and δ2H analysis of benzenes and alkylated derivatives were used to interpret both the impact of different sources on a contaminant plume and the presence of degradation processes. The different contaminant sources could be distinguished based on their combined δ13C–δ2H signature of the benzene, toluene, ethylbenzene and xylenes (BTEX) dissolved in the groundwater. Despite this source differentiation, plume characterisation was not possible due to the complex mixing of the respective contaminant plumes. Furthermore, the original isotope signatures of the sources were not preserved across these plumes. To estimate the level of in situ biodegradation independently from concentration data, the Rayleigh equation was used. Although current literature identifies the application of CSIA as very promising in the frame of characterising organic groundwater pollution, this study has indicated that this approach can be limited with respect to successfully distinguish the different plumes and their relation to the known source zones.