Electroosmotic flow (EOF) is commonly utilized in microfluidics. Because the direction of the EOF can be determined by the substrate surface charge, control of the surface chemical state offers the potential, in addition to voltage control, to direct the flow in microfluidic devices. We report the use of polyelectrolyte multilayers (PEMs) to alter the surface charge and control the direction of flow in polystyrene and acrylic microfluidic devices. Relatively complex flow patterns with simple arrangements of applied voltages are realized by derivatization of different arms of a single device with oppositely charged polyelectrolytes. In addition, flow in opposite directions in the same channel is possible. A positively derivatized plastic substrate with a negatively charged lid was used to achieve top-bottom opposite flows. Derivatization of the two sides of a plastic microchannel with oppositely charged polyelectrolytes was used to achieve side-by-side opposite flows. The flow is characterized using fluorescence imaging and particle velocimetry.