Water management is of critical importance in a proton exchange membrane (PEM) fuel cell, in particular, those based on a sulfonic acid polymer, which requires water to conduct protons. Yet there are limited in situ studies of water transfer through the membrane and no data are available for water transfer due to individual mechanisms through the membrane in an operational fuel cell. Thus it is the objective of this study to measure water transfer through the membrane due to each individual mechanism in an operational PEM fuel cell. The three different mechanisms of water transfer, i.e., electro-osmotic drag, diffusion and hydraulic permeation are isolated by specially imposed boundary conditions. Therefore water transfer through the membrane due to each mechanism is measured separately. In this study, all the data is collected in an actual assembled operational fuel cell. The experimental results show 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 the other two mechanisms. The data for water transfer due to diffusion through the membrane are in good agreement with some of the ex situ data in the literature. The data for electro-osmosis show that the number of water molecules dragged per proton increases not only with temperature but also with current density, which is different from existing data in the literature. The methodology used in this study is simple and can be easily adopted for in situ water transfer measurement due to different mechanisms in other PEM fuel cells without any cell modifications.