• The Bernstein Project The Watermark Initiative Project participated by invitation in the planning events that led to formation of the Bernstein Project, and has been actively engaged in the development of the Bernstein Paper Portal as a collaborating associate. The Bernstein Project adopted the WAI's previously published plans for a distributed database system and incorporated the implementation of the distributed database into its goals. The WAI is focusing its own work on development of its database, the International Paper Registry (IPR) for use in the distributed database system.
• The Digital Scriptorium Project. The database schema and data dictionary of the WAI has been designed with the intention of compatibility with the Digital Scriptorium, which appears to represent the emerging standard for www-based database description of medieval manuscripts.
• Catalogi Codicum Montis Athonis The Mount Athos Greek Manuscripts Catalog Project, a cooperative project of the Ancient Biblical Manuscripts Center, Claremont California, and the Patriarchal Institute for Patristic Studies, Thessaloniki, Greece
• The Grete Herball Project. This project, a collaboration of The Watermark Initiative, The Royal Horticultural Society Libraries and the University of London's School of Advanced Study, consists of the digital imaging by Ian Christie-Miller of the papers used in surviving copies of the Grete Herball, and the on-line publication of these images and the related paper descriptions using the International Paper Registry. It is a scholarly work in its own right, and a pilot project for the development of both the Early Book Imaging System, the Advanced Paper Imaging System developed by Christie-Miller, and the WWW version of the International Paper Registry.

A central objective of the Watermark Initiative in its relationships with these projects is "interoperability" -- that it should link transparently to various kinds of projects in which paper-bearing objects are of central importance.