The non-aqueous phase-liquid (NAPL)-contaminated aquifer at a major refinery site in Mexico was investigated. Owing to the depth of the contaminated aquifer section (NAPL source zone) of over 100 m below the surface, the actual aquifer material was not accessible for sampling. Information on the residual NAPL contamination of the aquifer could only be obtained indirectly by analysing groundwater samples from a few wells available at the site. To tackle the problem, an approach alternative to conventional groundwater analysis for dissolved NAPL was chosen. For evaluating the recent contamination and estimating its probable future development, the radioisotope radon-222 and the stable isotopes 13C, 34S and 18O were used as naturally occurring contamination tracers and process indicators. Radon was used as partitioning tracer for the approximate localization and semi-quantitative assessment of the NAPL source zone. The stable isotopes were used as indicators for naturally occurring biodegradation processes, which might potentially be implemented into future remediation schemes.