Capnography records CO2 partial pressure in exhaled breath as a function of time or exhaled volume. Time-based capnography, which is our focus, is a point-of-care, noninvasive, effort-independent and widely available clinical monitoring modality. The generated waveform, or capnogram, reflects the ventilation-perfusion dynamics of the lung, and thus has value in the diagnosis of respiratory conditions such as chronic obstructive pulmonary disease (COPD). Effective discrimination between normal respiration and obstructive lung disease can be performed using capnogram-derived estimates of respiratory parameters in a simple mechanistic model of CO2 exhalation. We propose an enhanced mechanistic model that can capture specific capnogram characteristics in congestive heart failure (CHF) by incorporating a representation of the inertance associated with fluid in the lungs. The 4 associated parameters are estimated on a breath-by-breath basis by fitting the model output to the exhalations in the measured capnogram. Estimated parameters from 40 exhalations of 7 CHF and 7 COPD patients were used as a training set to design a quadratic discriminator in the parameter space, aimed at distinguishing between CHF and COPD patients. The area under the ROC curve for the training set was 0.94, and the corresponding equal-error-rate value of approximately 0.1 suggests classification accuracies of the order of 90% are attainable. Applying this discriminator without modification to 40 exhalations from each CHF and COPD patient in a fresh test set, and deciding on a simple majority basis whether the patient has CHF or COPD, results in correctly labeling all 8 out of the 8 CHF patients and 6 out of the 8 COPD patients in the test set, corresponding to a classification accuracy of 87.5%.