Radiolabelled assays and compound-specific stable isotope analysis (CSIA) were used to assess methyl tert-butyl ether (MTBE) biodegradation in an unleaded fuel plume in a UK chalk aquifer, both in the field and in laboratory microcosm experiments. The 14C-MTBE radiorespirometry studies demonstrated widespread potential for aerobic and anaerobic MTBE biodegradation in the aquifer. However, δ13C compositions of MTBE in groundwater samples from the plume showed no significant 13C enrichment that would indicate MTBE biodegradation at the field scale. Carbon isotope enrichment during MTBE biodegradation was assessed in the microcosms when dissolved O2 was not limiting, compared with low in situ concentrations (2 mg/L) in the aquifer, and in the absence of O2. The microcosm experiments showed ubiquitous potential for aerobic MTBE biodegradation in the aquifer within hundreds of days. Aerobic MTBE biodegradation in the microcosms produced an enrichment of 7‰ in the MTBE δ13C composition and an isotope enrichment factor (ε) of −1.53‰ when dissolved O2 was not limiting. However, for the low dissolved O2 concentration of up to 2 mg/L that characterizes most of the MTBE plume fringe, aerobic MTBE biodegradation produced an enrichment of 0.5–0.7‰, corresponding to an ε value of −0.22‰ to −0.24‰. No anaerobic MTBE biodegradation occurred under these experimental conditions. These results suggest the existence of a complex MTBE-biodegrading community in the aquifer, which may consist of different aerobic species competing for MTBE and dissolved O2. Under low O2 conditions, the lower fractionating species have been shown to govern overall MTBE C-isotope fractionation during biodegradation, confirming the results of previous laboratory experiments mixing pure cultures. This implies that significant aerobic MTBE biodegradation could occur under the low dissolved O2 concentration that typifies the reactive fringe zone of MTBE plumes, without producing detectable changes in the MTBE δ13C composition. This observed insensitivity of C isotope enrichment to MTBE biodegradation could lead to significant underestimation of aerobic MTBE biodegradation at field scale, with an unnecessarily pessimistic performance assessment for natural attenuation. Site-specific C isotope enrichment factors are, therefore, required to reliably quantify MTBE biodegradation, which may limit CSIA as a tool for the in situ assessment of MTBE biodegradation in groundwater using only C isotopes.