In this work we characterize electrokinetics in hydrophobic microfluidic substrates with aqueous working solutions as a function of the history of the fluid-solid interface. We utilize time-resolved streaming potential and current monitoring experiments to show that the electrokinetic potential in Zeonor and TOPAS substrates is a function of time after (i) initial formation of the fluid-solid interface, and (ii) after ethanol-water solvent exchanges. In these systems, the electrokinetic potential is initially large in magnitude, and decays exponentially with a time constant that is on the order of hours. We further show that the kinetics of the decay are affected by exposure to electric fields, and the ambient pressure of air surrounding the system. These data suggest that the state of dissolved gases in solution must be considered among the parameters that affect the electrokinetic potential of hydrophobic surfaces with aqueous solutions.