This investigation is devoted to the influences of non-uniform wall characteristics on the surface adsorption-desorption rates in an electrokinetic microarray. Utilizing already explored electroosmotic and electrophoretic velocities, the species transport equations are solved by a finite-volume-based numerical approach. Uniform, sinusoidal, and pulse-like distributions of the zeta potential are considered in the analysis. The developed model is validated by comparing the results with those of two analytical solutions that are derived for limiting conditions. The results reveal that, in some cases, the surface charge heterogeneity can reduce the saturation time by more than 60%. The efficacy of the surface charge heterogeneity is limited to high Damkohler numbers and its effects are negligible for small values of this parameter. Whereas the impact of non-uniform surface characteristics is amplified by increasing the Peclet number, it is reduced by increasing either of the channel length to radius ratio or the electrophoretic mobility of the analytes.