A method for controlling the flow of natural gas and refrigerant in the main heat exchanger of a natural gas liquefaction facility. The method provides for the automated control of a flow rate of a natural gas feed stream through a heat exchanger based on one or more process variables and set points. The flow rate of refrigerant streams through the heat exchanger is controlled by different process variables and set points, and is controlled independently of the flow rate of the natural gas feed stream.