National Sustainable Offshore Aquaculture Act of 2009

National Sustainable Offshore Aquaculture Act of 2009 - Directs the Secretary of Commerce to establish an Office of Sustainable Offshore Aquaculture in the National Marine Fisheries Service at National Oceanic and Atmospheric Administration (NOAA) headquarters and at satellite offices in each of NOAA's regional fisheries offices.

Requires the Office to establish a Sustainable Offshore Aquaculture Advisory Board. Directs the Secretary to: (1) establish and maintain in the Office an aquaculture database; and (2) make the database available to the public but protect proprietary information of owners and operators of offshore aquaculture facilities.

Requires, for permit issuance, a regional programmatic environmental impact statement under the National Environmental Policy Act of 1969 (NEPA) for each Regional Fishery Management Council and a separate environmental review under NEPA.

Prohibits engaging in offshore aquaculture without a permit under this Act and authorizes the Secretary to issue such permits.

Requires the Secretary to: (1) assess application and annual fees with respect to such permits that are sufficient to pay the costs of issuing, monitoring, and enforcing such permits; and (2) assess resource rental fees to recover from permittees a reasonable portion of the value of the use under the permits of ocean resources held in public trust.

Directs the Secretary to establish and conduct a research program to guide the sustainable development of offshore aquaculture, including regarding: (1) industry expansion that ensures ecological sustainability and functional ecosystems and fisheries; and (2) cost-effective solutions to environmental and socioeconomic impacts. Requires a related competitive, peer-reviewed grant program.

Prohibits permit issuance: (1) for a species having a fishery management plan under the Magnuson-Stevens Fishery Conservation and Management Act (Magnuson Act) or in a Regional Fishery Management Council's jurisdiction unless all relevant Councils recommend approval; or (2) if opposed by the nearest coastal state.

Regulates the relationship of this Act to the Magnuson Act, the Outer Continental Shelf Lands Act, and the Coastal Zone Management Act.

Regulates the assessment and liability for natural resource damages associated with offshore aquaculture.