A dialysis system includes a disposable cassette including a flexible sheet and a plurality of dialysis fluid pathways, a plurality of actuators operable with the flexible sheet to direct dialysis fluid through the plurality of dialysis fluid pathways, and a controller configured to (i) determine at least one limitation of the plurality of dialysis fluid pathways, (ii) generate a flow schedule indicating how dialysis fluid should be directed through the plurality of dialysis fluid pathways in accordance with the at least one limitation, and (iii) control the plurality of actuators so that dialysis fluid is pumped through the plurality of dialysis fluid pathways according to the flow schedule.