Water flow in the vadose zone is often modeled as a single-phase flow where the air phase is assumed to be free to flow. Although this is a fair assumption in many practical cases, there are a number of applications where the free flow of air is hindered due to various causes. Air phase that is not free to flow in the subsurface can lead to a decreased infiltration rate or changes in water flow paths. In this study, we improved methods for measuring air pressure in wet soil, and demonstrated its applicability to investigate how the air phase can play a critical role in heterogeneous soil under certain conditions. To achieve this, we performed two sets of experiments. In the first set of experiments, we tested seven different porous material–hydrophobic treatment combinations for air pressure measurement in soils that were initially water saturated. In the second set of the experiment, drainage was induced in a layered column where a layer of coarse sand was overlaid by finer sand. Air pressure was monitored using the method selected based on the results of the first experiment. As the drainage proceeded, the layer of coarse sand released water when the air phase penetrated through the fine sand layer. The air pressure in the coarse layer rapidly decreased (became negative) as the water was released. The results demonstrated that the improved air pressure measuring method successfully indicated a decrease in air pressure during the drainage, and that the single-phase approach where only the water pressure is considered becomes invalid for cases where free air flow is hindered and water–air interaction is significant.