The effect of physical heterogeneity on the electrokinetic (EK) transport of nitrate, an electron acceptor frequently used for anaerobic biodegradation, was investigated experimentally within saturated granular porous media comprising two layers of high and low hydraulic conductivity (K) material. Two hypotheses were tested: firstly, that the presence of layered physical heterogeneity will generate non-uniformities in the electric field; and secondly that this would create non-uniform electromigration of ions resulting in an additional nitrate flux into the lower-K layer. Experiments were conducted in bench-top test cells that contained electrode and sediment chambers. An aqueous nitrate solution (0, 0.1, 1 and 5 g-NO3 L-1) was added at the cathode and the experiments run with an idealised mixture of glass beads and kaolinite, and natural sediment and kaolinite. A constant current (1.6 A m(-2)) was applied in all experiments. Results showed elevated voltage differences between layers in heterogeneous experiments compared to equivalent homogenous experiments. Furthermore, nitrate concentrations are elevated in the low-K material in heterogeneous compared with homogeneous systems. Using predicted values this is shown to be a function of a transverse flux associated with the voltage difference between layers. The importance of this phenomena at field scale for delivery of an amendment (i.e., electron acceptor, donor or nutrient) by EK for bioremediation is presented in an electron balance model. Overall, this research establishes and quantifies a previously unreported important phenomenon in the electrokinetic transport literature that enhance the application of this technology for bioremediation of contaminated aquifers. (C) 2016 The Authors. Published by Elsevier Ltd.