A system for determining a parameter of respiratory mechanics in the presence of an intrinsic positive end-expiratory pressure during a ventilator support of a patient is provided. The system includes a computer system that comprises one or more in physical processors programmed with computer program instructions which, when executed cause the computer system to: determine breath segmentation data from airway flow information of the patient and airway pressure information of the patient; and determine the parameter of respiratory mechanics in the presence of the intrinsic positive end-expiratory pressure using the determined breath segmentation data. The parameter of respiratory mechanics includes one or more of the following: respiratory resistance, respiratory elastance, respiratory compliance, the intrinsic positive end-expiratory pressure, a pressure inside the alveoli, and an equivalent pressure generated by the respiratory muscles of the patient.