A system and method for regulating cooperatively the pressures and flows of input vessels such as both the portal vein and hepatic artery for the liver. This invention solves problems of less-than-therapeutic portal vein flow during perfusion preservation by implementing cooperative regulation between the inputs, e.g., portal vein and hepatic artery pumping systems, on an organ preservation apparatus. It includes an algorithm that adapts to the situation wherein the portal vein has reached minimum flow and maximum pressure. The cooperative regulation algorithm senses the problem with the portal vein and solves it by adjusting the hepatic artery flow conditions.