A system or method controls total fluid loss (TFL) in a patient undergoing hemofiltration therapy administered through an extracorporeal circuit by frequently calculating and storing a retrievable value representing TFL. At session start or restart, the value is read to determine whether TFL is out of tolerance, and if so, fluid balance is restored before administering a prescribed therapy. The TFL value is calculated during therapy by measuring fluid added to the circuit and fluid removed from the circuit, and the result is stored as an updated value. If TFL drifts out of tolerance fluid flow rates may be temporarily changed until a desired fluid balance is restored. The system may include a microprocessor based advanced controller receiving the fluid measurements as feedback for regulating substitution fluid and filtrate flow rates, and updating the TFL, value in non-volatile memory.