In fuel cell catalyst layers (CLs), the ionomer plays roles as a binder and proton conductor. The ionomer requires hydration for enabling proton transport; however, the accumulation of excess liquid water in CL pores hinders oxygen diffusion. Therefore, a key to the improvement of CLs is understanding the distribution and the quantity of water in an operando fuel cell. However, there is a lack of information on the water content in conventional Pt-based CLs during operation, especially within the ionomer phase. Here, we present the application of high-resolution operando small-angle neutron scattering (SANS) on custom fuel cells to probe the CL water content. Using this technique, we quantified liquid water saturation and ionomer nanostructure (swelling) in in situ CLs, unique information not accessible via conventional diagnostic tools such as imaging. Even at a low current density (150 mA/cm2), water was observed in the cathode CL as liquid and adsorbed in the ionomer. Improving the understanding of water management in the CL is of high interest in fuel cell community, and our results confirm that operando SANS will be indispensable for the development of catalysts and ionomer-based CLs.