Abstract Water sorption isotherm of catalyst layers in polymer electrolyte fuel cells is analyzed by a mathematical model. The model takes into account multi-layer water adsorption on adsorption sites and capillary condensation in hydrophilic pores. The detailed structures of CLs including the pore size distribution, volume fraction of hydrophilic pores, and ionomer coverage over carbon supports and Pt surface are thoroughly considered. Quantitative estimation of water uptake at different locations in CLs as a function of vapor activity is successfully achieved. The model reveals that water adsorption in CLs firstly takes place on the adsorption sites such as side chains in Nafion® ionomer, Pt surface, and surface groups on carbon supports at low vapor activity. The primary pores are filled with capillary condensed water at activity of 0.4. The condensation of water in the secondary pores is observed at activity from 0.9 to 1. The wetting property of the primary pores strongly depends on carbon materials, while surface of the secondary pores is found to show the hydrophobic nature irrespective of carbon materials. The amount and location of water in CLs are correlated with electrochemical double layer and effective proton conductivity.