Temperature compensation is applied to correct for temperature mismatch between a reference chamber and a disposable chamber in a pneumatic pumping system for dialysis fluid for peritoneal dialysis. The mismatch creates an error in the calculation of pumping volume of dialysate fluid. Applying a correction for the temperature mismatch helps to more precisely control the volume of dialysate that is metered to the patient. Also disclosed are ways to keep temperatures constant and to use temperature sensors to accurately measure the temperatures of the chambers. In other aspects, the temperature of the dialysate fluid itself may be measured and used to apply a correction to the volume of fluid that is pumped to the patient.