Certain potentially unfavorable aspects of aqueous-based deacidification appear to have provided the main motivation for widespread adoption of non-aqueous deacidification systems.  For instance, if a book is dropped into a sink of water, the paper can become wavy  and a lengthy drying period may be needed.  Each individual page tends to expand when it is wetted by water, increasing its thickness.  Such swelling may exceed the binder’s capacity, causing the book to break.  When deacidifying individual sheets of paper documents, such development of waviness can be avoided by drying the sheets individually against a smooth surface or by other means of restraint during drying.  In the case of books, freeze-drying has been used successfully to avoid deformation of pages.  To overcome these issues concerning the aqueous treatment of bound books, it is common practice to remove and replace the original binder for the book, allowing the pages to be treated and dried individually.  Advantages of this approach include optional washing of the pages, the ability to directly neutralize acidic groups present in the material, the ability to apply pH-buffering agents and/or alkaline particles, the ability to treat the paper with reducing agents such as borohydride, and the opportunity to apply dissolved starch or other hydrophilic polymers able to increase the strength of the paper.  The down-side of such an approach is that it requires a considerable expense and time to disassemble and reassemble each treated book.

Other concerns about aqueous treatment include possible bleeding or dissolution of water-susceptible print colorants, a tendency of paper to become more bulky after a cycle of wetting and drying, and the sticking together of pages after redrying of bound volumes, especially if the paper had been coated during its manufacture.  For all of these reasons, when bound volumes need to be acidified, non-aqueous deacidification programs or treatments involving freeze drying processes generally have been selected.