United States Ferry Systems Investment Act of 2009 - Authorizes appropriations to the Secretary of Transportation for FY2010-FY2015 for construction of ferry vessels and ferry terminal facilities. Revises general requirements and the formula for the allocation of such funds to ferry systems and public entities responsible for developing ferries.
Includes ferries within the federal clean fuels program.
Directs the Secretary of Transportation to establish within the Department of Transportation a Ferry Joint Program Office to: (1) coordinate federal programs affecting ferry vessel and ferry facility construction, maintenance, operations, and security; and (2) promote ferry service as a component of the U.S. transportation system.
Requires the Secretary to: (1) ensure that the national ferry database is consistent with the national transit database maintained by the Federal Transit Administration; and (2) award a grant to a college to establish a National Ferry Transportation Institute for research, development, and training programs relating to U.S. ferry transportation systems.