This disclosure describes systems and methods for compensating for inelastic and elastic leaks in a ventilation system. The disclosure describes a model-based enhancement to conventional flow triggering and cycling methodologies that improves the timing and patient work of flow-based triggering and cycling performance. The methods and systems described herein compensate for the leak condition and minimize additional effort a patient has to exert to generate the same patient synchrony and comfort level compared to no leak condition. One method described includes calculating an elastic leakage and an inelastic leakage based on current measurements of pressure and flow in the ventilation system and then estimating a leak-compensated lung flow using the inelastic and elastic leaks and pneumatic attributes of the patient-ventilator system.