Water management is of critical importance in a proton exchange membrane (PEM) fuel cell. Yet there are very limited studies of water transfer through the membrane and no data are available for water transfer due to individual mechanisms through the membrane electrode assembly (MEA) in an operational fuel cell. Thus it is the objective of this study to measure water transfer through the MEA due to different mechanisms through the membrane electrode assembly (MEA) of an operational PEM fuel cell. The three different mechanisms of water transfer, i.e., electro-osmotic drag, diffusion and hydraulic permeation were isolated by specially imposed boundary conditions. Therefore water transfer through the MEA due to each mechanism could be measured separately. In this study, all the data were collected in an actual assembled operational fuel cell, and some of the data were collected while the fuel cell was generating power. The measured results showed that water transfer due to hydraulic permeation, i.e. the pressure difference between the anode and cathode is at least an order of magnitude lower than those due to other two mechanisms. The data for water transfers due to electro-osmosis and diffusion through the MEA are in good agreement with some of the data and model predications in the literature for the membrane. The methodology used in this study is simple and can be easily adopted for in-situ water transfer measurement due to different mechanisms in actual PEM fuel cells without any cell modifications.