In the fuel cell catalyst layers (CLs), the ionomer plays roles as a binder and a conductor for protons. It is now known that the ionomer not only forms aggregates between the catalyst agglomerates of the porous structure of the CLs, but it also forms a few nanometer thick thin film covering the surface of this catalyst. In this latter form, it modifies the specific activity of the catalyst by altering the structure and behavior of the electrochemical double layer, and it hinders the oxygen transport toward the catalytic sites. In addition, the nanostructure and functional transport properties of O2 and protons of the ionomer depends on its water content which increases with water activity. Especially, the ionomer must be sufficiently hydrated to enable proton transport from the membrane toward the active sites through the CLs and ensure a proper utilization of the electrochemical surface area. However, excess liquid water accumulation in the pores of the CL hinders oxygen diffusion and should be avoided. Therefore, it is necessary to understand the distribution and the quantity of water, being either within the ionomer or in the pores of the catalyst layers, during fuel cell operation to improve their design and constituents. Very recently, and based on our former experience, we pushed forward the in situ and in operando Small Angle Scattering techniques to quantify the water content and ionomer swelling in fuel cell CLs during operation. In this work, we report the effect of the conditioning and operating conditions on the ionomer behavior.