A method is provided for calibrating a pump during a blood separation procedure that has at least a first state or phase where fluid is flowed to or from a reservoir by action of the pump. The state or phase of the procedure may be a priming state, a draw state, a separation state and a return state, and the pump calibration may be performed between consecutive performances of the same procedure state. The calibration is based on a variance between the volume of fluid predicted to be processed by the pump for the given state of the procedure and the actual volume processed based on the change of weight of the reservoir. Recalibration of the pump, if necessary, is accomplished before the performance of a second phase of the procedure where fluid is flowed to or from a reservoir by action of the pump or a subsequent performance of the first phase is commenced.
