A system and method is provided for controlling the operation of secondary coolant pump(s) in a refrigeration system having a secondary coolant system that circulates the coolant to applicable cooling loads, and a primary refrigeration system that chills the coolant in the secondary coolant system. The system and method for controlling the pumps measures the pressure of the plurality of secondary coolant fluid loops, sorts the measurements to identify a secondary coolant fluid loop with a pressure farthest from a setpoint, and adjusts pump speed to compensate for the critical loop (i.e., the secondary coolant fluid loop with a pressure furthest from the setpoint).