Electrokinetics (EK) was applied to enhance biodegradation of toluene in the low hydraulic conductivity (K) zone of a physically heterogeneous water-saturated granular porous media. The hypothesis tested was that EK transport processes, which operate independently of advection, can deliver a limiting amendment, nitrate, across a high-K–low-K boundary to stimulate bioremediation. Two types of experiment were evaluated: (1) bench-scale tests that represented the active EK system and physically heterogeneous sediment configuration; (2) microcosms that represented biodegradation in the bench-scale tests under ideal conditions. The bench-scale experiment results showed a rapid decrease in toluene concentration during the application of EK that was attributed to electroosmotic removal from low-K zones. Comparison of toluene removal rates by electroosmosis and biodegradation (microcosm) confirmed that electroosmosis was the most effective mechanism under the conditions evaluated. Overall, this work challenges the original hypothesis and indicates that, at the field scale, the most favourable conditions for biodegradation are likely to be achieved by applying EK to increase contaminant flux across the low-K–high-K boundary (out of the low-K zone) and allowing biodegradation to occur in the high-K zone either by natural attenuation or enhanced by amendment addition.Supplementary material: Supplementary material is available at https://doi.org/10.6084/m9.figshare.c.5174554