Oxygen dissolved in water is a cause of corrosion in heating installations. On the other hand, in the production of beverages such as beer, it leads to the oxidation of organic matter, decreasing the quality of the product. Therefore, its content must be substantially reduced. In this work, the catalytic deoxygenation of water using a palladium catalyst is studied. The catalyst consists of palladium ion-exchanged on a weak-basic macroporous resin. This work addresses the catalytic deactivation and regeneration of this type of catalyst, comparing results obtained in the laboratory with those obtained from an industrial reactor used to deoxygenate water for beer production. Two deactivation mechanisms are observed: (i) In the short term, the deposition of organic material (humic acids) coming with the water is responsible for activity lost; (ii) in the long term, the cause of the irreversible deactivation is the palladium leaching that occurs during the cleaning-in-place procedure, which is carried out with sodium hydroxide solution at 60 °C. This deactivation occurs in the presence of dissolved oxygen and is strongly favored by the presence of chlorine in the water. This study indicates the conditions necessary to regenerate the catalyst and to largely improve the stability during operation−regeneration cycles.