The topmost atomic layers of electrocatalysts determine the mechanism and kinetics of reactions in many important industrial processes, such as water splitting, chlor-electrolysis or fuel cells. Optimizing the performance of electrocatalysts requires a detailed understanding of surface-state changes during the catalytic process, ideally at the atomic scale. Here, we use atom probe tomography to reveal the three-dimensional structure of the first few atomic layers of electrochemically grown iridium oxide, an efficient electrocatalyst for the oxygen evolution reaction. We unveil the formation of confined, non-stoichiometric Ir–O species during oxygen evolution. These species gradually transform to IrO2, providing improved stability but also a decrease in activity. Additionally, electrochemical growth of oxide in deuterated solutions allowed us to trace hydroxy-groups and water molecules present in the regions of the oxide layer that are favourable for the oxygen evolution and iridium dissolution reactions. Overall, we demonstrate how tomography with near-atomic resolution advances the understanding of complex relationships between surface structure, surface state and function in electrocatalysis.