This dissertation investigates liquid plug transport through the pulmonary airways. It includes three aspects: liquid delivery into the lungs, mucus clearance from the lungs, and plug dynamics in flexible small airways.Liquid plugs form in pulmonary airways during the process of liquid instillation in many clinical treatments. Studies have shown that treatment efficiencies may depend on how liquids distribute in the lung. Better understanding the fundamentals of liquid plug transport will reveal important system parameters governing the liquid distribution and facilitate treatment strategies. The plug propagation before reaching a bifurcation is studied computationally with the effects of gravity, plug speed and surfactant. Then the plug splitting through a symmetric bifurcation is studied experimentally and theoretically with different gravitational orientations, plug speeds, and downstream plug blockages. The liquid distribution is shown to be more homogeneous at larger volume, faster speed and lower gravitational effects.In diseases such as asthma and pulmonary emphysema, thickening of the liquid lining and lack of surfactant may cause mucus plugs to form and block the breathing pathway. Removing mucus from the lung is very essential to reduce threaten on patients’ life. Mucus plug propagation is studied computationally with various plug speed and different shear thinning properties. Larger pressure is found to be required to drive the mucus plug at larger plug speed and in greater shear thinning effect. The surfactant effect is then investigated and found helpful on the mucus removal.The plug propagation is studied in a microfluidic flexible channel experimentally, as a small airway model. Wall deformation is observed from the high negative pressure when plug propagates. The maximum wall deformation is found to increase with plug speed and plug length. Computations agree with the experiments and predict the higher stress and stress gradients on the flexible wall than the rigid one, which increase the potential risk on the cell damages.The results presented in this dissertation provide new insights into the physical mechanisms on liquid plug dynamics in pulmonary airways during liquid instillation and removal. Further investigation in both experiments and computations can be used to mimic the specific in-vivo situations.