Santa Ana River Water Supply Enhancement Act of 2009 - Amends the Reclamation Wastewater and Groundwater Study and Facilities Act to authorize the Secretary of the Interior, in cooperation with: (1) the Orange County Water District (the District), to participate in the design, planning, and construction of natural treatment systems and wetlands for the flows of the Santa Ana River, California, and its tributaries into the Prado Basin; (2) local governments, to assist agencies in projects to construct regional brine lines to export the salinity imported from the Colorado River to the Pacific Ocean; and (3) the Chino Basin Watermaster, the Inland Empire Utilities Agency, and the Santa Ana Watershed Project Authority, to participate in the design, planning, and construction of the Lower Chino Dairy Area desalination demonstration and reclamation project. Limits the federal share of total project costs. Prohibits using funds provided by the Secretary for operation and maintenance of the projects. Terminates the Secretary's authority to carry out this Act after 10 years.