The National Oceanic and Atmospheric Administration's (NOAA) Chesapeake Bay Office is a division of the National Marine Fisheries' Office of Habitat Conservation, which works to protect and restore coastal and marine habitat at the national level. The Office is also a key collaborator with NOAA's North Atlantic Regional Team, which integrates NOAA's program activities to address priorities at both the national and regional scale. 

NOAA has been a partner in Chesapeake Bay Program restoration and protection efforts since the signing of a Memorandum of Understanding with the U.S. Environmental Protection Agency in 1984. The NOAA Chesapeake Bay Office was formally established by Congress through the NOAA Authorization Act of 1992 (Public Law 102-567) and reauthorized in 2002 (Public Law 107-372) to be a focal point within NOAA for Chesapeake Bay initiatives and a conduit to apply NOAA’s wide range of capabilities to help address the problems and challenges of natural resource management in the Bay region.

On September 30, 2009, H.R. 1771, a bill to reauthorize the NOAA Chesapeake Bay Office, passed the U.S. House of Representatives. A related bill, S. 1224, is currently pending in the U.S. Senate. A bill that authorizes the Bay Watershed Education and Training (B-WET) Program, H.R. 3644 , also passed the U.S. House of Representatives on March 19, 2010.

More recently, NOAA has been charged by the President under Executive Order 13508 to begin a new era of shared federal leadership in protecting and restoring the Bay. The NOAA Chesapeake Bay Office will carry out Executive Order tasks through enhanced focus on four key topics (Fisheries, Habitats, Observations, and Education) as organized across the Office's three primary programs (Ecosystem Science, Coastal and Living Resource Management, and Environmental Literacy).

NOAA Chesapeake Bay Office staff includes personnel from NOAA's Fisheries Service, the National Ocean Service, the Office of Oceanic and Atmospheric Research, and the National Environmental Satellite, Data, and Information Service, as well as several contractors. Most staff are located in Annapolis, Maryland; others are positioned with partners at the Cooperative Oxford Laboratory in Oxford, Maryland, and at Nauticus in Norfolk, Virginia.