Zeolite Y is used in a wide field of catalysis because of its high surface area and strong acidity. Since flowing water is present in many catalytic liquid phase reactions, its impact was investigated. For that, the zeolite Y was treated with water at 200 °C and 42 bar in a flow reactor. The resulting characterization showed strong structural changes at high water flows. The typical zeolite structure was almost completely lost, but an amorphous phase similar to the faujasite framework was formed. Due to this, the characteristic micropores were destroyed (d = 0.7 nm, volume was reduced from 0.18 to 0.01 cm3/g) and small mesopores were created (d = 2–3 nm, volume was increased from 0.25 to 0.51 cm3/g). As a result, the specific surface area was not greatly reduced and was still at around 250 m2/g. In addition, the amount of octahedrally coordinated EFAl increased from 54 to 70% and a γ-Al2O3 as well as a kaolinite phase was observed. The formed tetrahedrally coordinated EFAl is responsible for EFAl-OH groups, which are strong Brønsted acid sites. In general, the total acid sites of the zeolite Y were not strongly reduced and the ratio of Lewis to Brønsted acid sites slightly increased from 70:30% to 80:20%. For all Al species, the oxygen coordination was strongly distorted. After water treatment, on Si a large number of coordinated OSi and OAl groups were substituted with OH groups. The ratio of Si to Al decreased from 1 to 0.7, because Si was dissolved out of the zeolite by the water. On the surface, it was vice versa, there the Si accumulated (the Si/Al ratio increased from 0.2 to 0.8), presumably as silica gel.