In this paper, we demonstrate, using both experiment and simulation, how sample zone conductivity can affect plug-plug mixing in small molecule applications of electrophoretically mediated microanalysis (EMMA). The effectiveness of in-line mixing, which is driven by potential, can vary widely with experimental conditions. Using two small molecule systems, the effects of local conductivity differences between analyte plugs, reagent plugs and the BGE on EMMA analyses are examined. Simul 5.0, a dynamic simulation program for CE systems, is used to understand the ionic boundaries and profiles that give rise to the experimentally obtained data for EMMA analyses for (i) creatinine determination via the Jaffe reaction, a reaction involving a neutral and an anion, and (ii) the redox reaction between gallate and 2,6-dichloroindophenol, two anions. Low sample conductivity, which is widely used in CE analyses, can be detrimental for in-line reactions involving a neutral reactant, as rapid migration of the ionic component across a low conductivity neutral zone results in poor reagent plug overlap and low reaction efficiency. Conversely, with two similarly charged reagents, a low conductivity sample plug is advantageous, as it allows field-amplified stacking of the reagents into a tight reaction zone. In addition, the complexity of simultaneously overlapping three reagent zones is considered, and experimental results validate the predictions made by the simulation. The simulations, however, do not appear to predict all of the observed experimental behavior. Overall, by combining experiment with simulation, an enhanced appreciation for the local field effects in EMMA is realized, and general guidelines for an advantageous sample matrix can be established for categories of EMMA analyses.