We utilize time-resolved electrokinetic measurements in order to study the electrokinetic properties of silica and TOPAS microfluidic channels as a function of the time history of the fluid-solid interface. in pressure-driven flow through TOPAS microchannels, the zeta-potential as inferred from streaming potential measurements decays exponentially by a factor of 1.5 with a characteristic decay time of 3 h after the initial formation of the fluid-solid interface. A similar exponential decay is observed immediately after water is exchanged for ethanol as the solvent in the system. In electroosmotically driven flow through TOPAS microchannels, the zeta-potential as inferred through current monitoring experiments was constant in time. No electrokinetic transients were observed in silica microchannels under these flow conditions.