Chesapeake Bay Science, Education, and Ecosystem Enhancement Act of 2009

Chesapeake Bay Science, Education, and Ecosystem Enhancement Act of 2009 - Amends the National Oceanic and Atmospheric Administration Authorization Act of 1992 to revise research, management, and program provisions of the Chesapeake Bay Office of the National Oceanic and Atmospheric Administration (NOAA).

States that the Director of the Office shall be responsible for the administration and operation of the Office and implementation of such Act.

Requires the Director to: (1) implement the program activities of the Chesapeake Executive Council; (2) ensure that projects have scientific and technical merit and have undergone appropriate peer review; (3) consult with the Council; and (4) report biennially to Congress and to the Secretary of Commerce regarding activities to protect the Chesapeake Bay.

Authorizes the Director to: (1) collaborate with scientific and academic institutions, state and federal agencies, nongovernmental organizations, and other constituents to support an integrated observations system for the Chesapeake Bay; (2) support the establishment and implementation of the Captain John Smith Chesapeake National Historic Trail; (3) incorporate the Chesapeake Bay Interpretive Buoy System into the Integrated Ocean Observing System regional network of observatories; (4) establish a Chesapeake Bay watershed education and training program (authorizes related grants); (5) establish a Chesapeake Bay coastal living resources management and habitat program to support management of priority Chesapeake Bay habitats and living resources, including oysters, blue crabs, and submerged aquatic vegetation; and (6) accept donations of funds, property, and services.

Authorizes FY2011- FY2014 appropriations for the Office and related activities.