Groundwater from a diesel fuel-contaminated site in Vienna, Austria, was treated in pilot-scale subsurface flow constructed wetlands. The study aims at quantifying the contribution of biodegradation to the total removal of diesel compounds by means of compound-specific isotope analysis (CSIA). This innovative approach requires a constant isotope fractionation during the microbial transformation reaction which leads to an enrichment of the heavy isotopes, i. e. 13C and 2H, in the remaining pollutant. Filter material and/or groundwater was incubated in laboratory microcosms and the aerobic degradation of n-decane, which was chosen as model compound for diesel hydrocarbons, was monitored. Isotope fractionation was absent in water saturated microcosms because only minor n-decane biodegradation took place. During n-decane biodegradation in moist filter material, on the other hand, small but variable isotopic fractionation factors were found. The different experimental set-ups give indications how mass transfer limitations of hydrophobic molecules might mask isotopic fractionation and the consequences for field applications of CSIA are discussed in detail.