A fluid pumping system with energy recovery features may provide feed water to a reverse osmosis unit. The system includes an electronic controller unit that regulates the output of three hydraulic pumps. Each hydraulic pump drives the movement of a piston in a cylinder. The pistons collectively deliver a generally constant flow of high pressure feed water. Valve bodies direct reverse osmosis concentrate to the back sides of the pistons. The electronic controller coordinates the output of the hydraulic pumps with the actuation of the valve bodies. Movement of the pistons is controlled, in part, by a feed back loop to verify the desired hydraulic pump output. Valve bodies are designed to begin closing when an associated piston velocity decreases. The valve body moves after a dwell period when an associated piston should not be moving. The piston and cylinder are designed for exposure to high salt-content water.