The international scope of the Tijuana River watershed, the diversity of habitats, and the range of human and physical problems facing the Reserve make it an area rich for study in both the life and social sciences. The Reserve serves as a site for research conducted by both Reserve staff as well as outside researchers.  The Reserve's research and monitoring programs are guided by national plans such the Reserve System Strategic Plan that identify goals, priorities, and implementation strategies for these programs, as well as research needs specific to the Tijuana River Reserve. This approach, when used in combination with the education and outreach programs, helps ensure the availability of scientific information that has long-term, system-wide consistency and utility for managers and members of the public to use in protecting or improving natural processes in their estuaries.

An overarching focus of the research and monitoring program at the Tijuana River Reserve is to conduct and facilitate adaptive management by coupling science with on-the-ground stewardship activities.  The reserve has long been a site for the development of adaptive approaches to the restoration of tidal salt marsh, and the long-term vision of the reserve's restoration program is to explicitly couple research with marsh creation activities.  In addition, the Research program is actively working on the ecology and management of exotic species within estuarine settings.