A bi-directional pump system that can be configured for a plurality of operating modes. The bi-directional pump system includes a plurality of bi-directional pumps each having their own valving system that are connected to a common high pressure manifold, a low pressure manifold and a suction manifold. Via the respective valve systems, each pump can be configured into: (1) a single-acting pumping mode; (2) a double-acting pumping mode; (3) an inactive free motion mode; and (4) an inactive rigid mode. One exemplary application of the bi-directional pump system is on an articulated wave energy conversion system that consists of three floating barges: a front barge, a center barge and a rear barge where the front barge and center barge are hingedly connected as are the center barge and the rear barge. A first set of the bi-directional pumps span the first hinge connection and the second set of bi-directional pumps span the second hinge connection. The bi-directional pump system intakes sea water and, using wave energy, outputs a high pressure flow of sea water for water desalination and/or for driving electrical generators.