The NOAA Chesapeake Bay Office is headquartered at the Annapolis City Marina in the Eastport neighborhood of Annapolis, Maryland. As the state capital, Annapolis is home to many state government and nonprofit partners.

The office is colocated with the main office of the Chesapeake Bay Program, a unique regional partnership that has led and directed the restoration of the Chesapeake Bay since 1983. NOAA has been a valued federal partner of the Chesapeake Bay Program since the signing of a memorandum of agreement with the U.S. Environmental Protection Agency in 1984.

The Annapolis location is within a short drive of the Washington, D.C., metro area, including NOAA's headquarters in Silver Spring, Maryland. This central location enables NOAA to interact with a wide variety of Bay constituencies and encourages close collaboration with other state, regional, and federal agencies and partners.