In one aspect, a peritoneal dialysis (PD) system includes a housing that receives a disposable cassette, a plurality of pinch valves that receive respective sections of fluid tubing of the disposable cassette, an air port that forms an airtight seal with an air line of the disposable cassette, an air pump that alternatingly pushes air out of the air port and pulls air in from the air port, and a computer processor that controls the plurality of pinch valves and the air pump such that the cassette performs a dwell phase in which the diaphragm pump pumps fresh dialysate from a dialysate bag to a heater bag, a fill phase in which the diaphragm pump pumps the fresh dialysate from the heater bag to a patient line, and a drain phase in which the diaphragm pump pumps spent dialysate form the patient to a drain.