Aqueous-phase postsynthetic modifications of the industrially important Y-type zeolite are commonly used to change overall acid site concentrations, introduce stabilizing rare-earth cations, impart bifunctional character through metal cation exchange, and tailor the distribution of Brønsted and Lewis acid sites. Zeolite Y is known to undergo framework degradation in the presence of both vapor- and liquid-phase water at temperatures exceeding 100 °C, and rare-earth exchanged and stabilized HY catalysts are commonly used for fluidized catalytic cracking due to their increased hydrothermal resilience. Here, using detailed spectroscopy, crystallography, and flow-reactor experiments, we reveal unexpected decreases in Brønsted acid site (BAS) density for zeolite HY following exposure even to room-temperature liquid water. These data indicate that aqueous-phase ion-exchange procedures commonly used to modify zeolite Y are impacted by the liquid water and its removal, even when fractional heating rates and inert conditions much less severe than standard practice are used for catalyst dehydration. X-ray diffraction, thermogravimetric, and spectroscopic analyses reveal that the majority of framework degradation occurs during the removal of a strongly bound water fraction in HY, which does not form when NH4Y is immersed in liquid water and which leads to reduced acidity in HY even when dehydration conditions much milder than those typically practiced are employed. Na+-exchanged HY prepared via room-temperature aqueous dissolution demonstrates that Brønsted acid sites are lost in excess of the theoretical maximum that is possible from sodium titration. The structural impact of low-temperature aqueous-phase ion-exchange methods complicates the interpretation of subsequent data and likely explains the wide variation in reported acid site concentrations and catalytic activity of HY zeolites with high-Al content.