San Francisco Estuary and Watershed Science is an open access, peer-reviewed journal that publishes research about the science and resource management of San Francisco Bay, the Sacramento-San Joaquin River Delta, and the upstream watersheds. The journal is published jointly by the CALFED Science Program, the California Digital Library eScholarship Repository, and the University of California—Davis John Muir Institute of the Environment.

There are five main objectives for San Francisco Estuary and Watershed Science:

1. To provide timely, Internet-based communication of peer-reviewed results of basic and applied research, as well as reviews and syntheses of information, principles, conclusions, and interpretations on key regional issues that specifically add to our understanding of the Bay-Delta estuary, its watershed and adjacent coastal ocean, and the management of their resources.
2. To provide the opportunity to publish longer reports, monographs, or special issues of multiple, related chapters covering complex subjects of both scientific and regional interest, and to provide access, as appropriate, to an archive of the underlying data.
3. To encourage publication of peer-reviewed reports on the findings and conclusions of studies conducted by management or regulatory agencies, for-profit and non-profit organizations, and other entities that otherwise might have very limited distribution.
4. To provide a forum for commentary, discussion, and debate on the scientific and management questions and issues pertaining to the science of the Bay-Delta estuary, its watershed and adjacent coastal ocean, and management of their resources.
5. To ensure that the content of San Francisco Estuary and Watershed Science is widely discoverable, searchable, and accessible through digital libraries, public Internet services, and other emerging information technologies.