Method of operating a pressure swing adsorption system having a plurality of parallel adsorber vessels and a plurality of valves and gas manifolds adapted to introduce gas into each adsorber vessel and withdraw gas from each adsorber vessel in a cyclic series of sequential process steps. A leaking valve may be identified by (1) determining a value of an operating parameter that is a function of the mass of gas provided to a receiving adsorber vessel or withdrawn from an adsorber vessel during a selected process step, portion of a process step, or series of process steps; (2) determining the deviation of the value of the operating parameter from a predetermined reference value; and (3) using the magnitude and direction of the deviation to determine whether any valves are leaking.