An automated, pre-programmed, multiplexed hydraulic valve actuator is described. The valve is membrane-based and normally open. In contrast to the membrane-based pneumatic valve, the hydraulic valve uses hydraulic liquid to exert the control pressure. The line pressure is controlled with a roller moving over a prefabricated topology. Multiple rollers, each traversing its own track, are assembled into a single carriage, which can be actuated either manually or with a single computer-controlled motor. A valve manifold and roller actuators are designed, fabricated, and tested to demonstrate three-way valve actuation in a pre-determined sequence. The performance of the valve is evaluated and the utility of the valve in the operation of a micro thermal cycler was demonstrated. Hydraulic controllers of the type described here can be operated either manually or under computer control and provide an inexpensive means of controlling flow in lab-on-a-chip devices.