Combining operando X-ray absorption spectroscopy and computational modelling shows unequivocally the distribution of active species in fresh and hydrothermally aged Cu-CHA and Cu-AEI zeolites during NH3-assisted selective catalytic reduction of NOx. Four principal species co-exist: CuI cations coordinated to NH3, CuI cations coordinated to the zeolite framework, solvated CuII cations, and framework-coordinated CuII species formed upon hydrothermal ageing of the zeolite sample. The CuIIst species were only observed in the hydrothermally aged zeolite samples and are formed upon the interaction of hydrated CuII cations with extra-framework Al generated during the hydrothermal treatment. These sites are inactive for NOx reduction, leading to a decrease in the catalytic performance of the hydrothermally aged zeolites. CuIIst formation was higher in Cu-CHA than in Cu-AEI. The better hydrothermal stability of Cu in the AEI framework is attributed to the tortuous channel structure of AEI that hinders the migration of hydrated CuII cations during hydrothermal ageing.