In high temperature polymer electrolyte fuel cells, phosphoric acid migration induces flooding of the anode gas diffusion layer at high current densities. The present study focuses on determining the influence of phosphoric acid flooding of the anode GDL on hydrogen mass transport limitations. Two methods for quantifying the performance losses at high current densities, related to acid migration, are discussed: anodic limiting current density measurements and electrochemical impedance spectroscopy. It is demonstrated that the limiting current measurements, the common method for determining transport resistances, is unable to detect the changes induced by acid migration, due to the transient time required when switching to the required low hydrogen concentrations, while EIS is able to capture the changes induced by acid migration because it is faster and less invasive. For diluted hydrogen, an increase of the transport resistance is measured, however the effect on the cell performance is negligible. The time constants for anode GDL flooding and de-flooding are determined based on the EIS data and found to be 8.1 +/- 0.1 min for flooding and about 5.8 +/- 0.9 min for de-flooding under the applied conditions.