A microfluidic platform containing charged hydrogels is used to investigate the effect of geometry on charge transport in electrodialysis applications. The influence of heterogeneity on ion transport is determined by electrical characterization and fluorescence microscopy of three different hydrogel geometries. We found that electroosmotic transport of ions towards the hydrogel is enhanced in heterogeneous geometries, as a result of the inhomogeneous electric field in these systems. This yields higher ionic currents for equal applied potentials when compared to homogeneous geometries. The contribution of electroosmotic transport is present in all current regimes, including the Ohmic regime. We also found that the onset of the overlimiting current occurs at lower potentials due to the increased heterogeneity in hydrogel shape, owing to the non-uniform electric field distribution in these systems. Pinning of ion depletion and enrichment zones is observed in the heterogeneous hydrogel systems, due to electroosmotic flows and electrokinetic instabilities. Our platform is highly versatile for the rapid investigation of the effects of membrane topology on general electrodialysis characteristics, including the formation of ion depletion zones on the micro-scale and the onset of the overlimiting current.