The healthy human respiratory tract is lined with a pseudostratified epithelia composed of ∼80% ciliated cells and ∼20% goblet cells. These cells produce and are bathed by a layer of airway surface liquid (ASL), which plays a critical role in lung defense by helping to maintain the sterility of the lung. This layer is composed of two phases: the mucus layer which functions to trap particulates, bacteria, and viruses, and the underlying periciliary liquid layer (PCL), which provides hydration, enabling mucus transport and clearance. This chapter describes the methods used to measure the structure and height of the ASL by XZ confocal microscopy and mucus transport rates using epifluorescent microscopy in live airway cultures. Furthermore, we also demonstrate that these methods are also applicable in novel ways to probe the ultrastructure of the airways including the establishment of pH gradients and the ability of the apical membrane glycocalyx in excluding larger molecules from the cell surface.