PEM electrolysis has gained a lot of attention in recent years due to its ability to produce clean, sustainable hydrogen. One of the crucial steps toward optimizing hydrogen production is understanding the role of operating conditions on performance; in particular, understanding mass transport effects is crucial for optimizing the operation of a PEM electrolyzer. In this article we measured and modeled mass transport losses in a single-cell PEM electrolyzer, as a function of pressure and water flow, using EIS. We found that pressure and water flow cause larger mass transport losses on the cathode. Moreover, we measured a more considerable effect with pressure than with water flow, which we interpret as a consequence of pressure-dependent bubble detachment sizes and an increase in the diffusion path for bubble nucleation. Furthermore, we found a dependence of the mass transport overpotential on different MEA design parameters, such as electrode thickness.