A gas flow metrology system for a substrate processing system includes N primary valves selectively flowing gas from N gas sources, respectively, where N is an integer. N mass flow controllers are connected to the N primary valves, respectively, to flow N gases from the N gas sources, respectively. N secondary valves selectively flow gas from the N mass flow controllers, respectively. A gas flow path connects the N secondary valves to a flow metrology system located remote from the N secondary valves, wherein the gas flow path includes a plurality of gas lines. A controller is configured to perform a hybrid flow metrology by selectively using a first flow metrology and a second flow metrology that is different from the first flow metrology to determine an actual flow rate for a selected gas at a desired flow rate from one of the N mass flow controllers.