This paper presented a parametric experimental study of electrokinetic instability phenomena in a cross-shaped configuration microfluidic device with varying channel depths and conductivity ratios. The flow instability is observed when applied electric field strength exceeds a certain critical value. The critical electric field strength is examined as a function of the conductivity ratio of two samples liquid, microchannel depth, and the treatment of microchannel wetted surface. It is found that the critical electric field strengths for the onset of electrokinetic instability are strongly dependent on the conductivity ratio of two samples liquid, and decrease as the channel depths increasing of microfluidic devices. In the present study, the surface inside microchannels is treated utilizing hydrophilic and hydrophobic organic-based SOG (spin-on-glass) nanofilms for glass-based microchips. The experimental results indicate that no significant difference for the critical electric fields for the onset of electrokinetic instability phenomena in both hydrophilic and hydrophobic SOG coating in the surface of microchannels. The critical electric fields for the onset of electrokinetic instability phenomena are slightly lower in both SOG coated cases in compare with that of the non-coated microchannel.