Water Protection and Reinvestment Act of 2009

Water Protection and Reinvestment Act of 2009 - Amends the Internal Revenue Code to establish in the Treasury the Water Protection and Reinvestment Trust Fund (Trust Fund) to support investments in clean water and drinking water infrastructure. Imposes through 2015: (1) an excise tax on the sale of containers of water-based beverages, water disposal products, and pharmaceutical products; and (2) a clean water tax on corporations. Appropriates revenues raised from such taxes to the Trust Fund.

Directs the Administrator of the Environmental Protection Agency (EPA) to allocate amounts from the Trust Fund for specified clean and safe drinking water programs.

Amends the Federal Water Pollution Control Act and the Safe Drinking Water Act to: (1) expand the types of projects eligible for funding by state revolving loan funds; and (2) set forth additional criteria for states in developing priorities for assistance under such Acts; and (3) provide for technical assistance to community water systems and small water treatment works.

Authorizes the Administrator to make grants to: (1) increase the security of community water systems and water treatment works; (2) hire certified wastewater treatment operators; and (3) control sewer overflow.

Requires the Administrator to make grants to: (1) support efforts by water systems to increase energy efficiency, reduce greenhouse gas emissions, and mitigate the impacts of climate change; (2) establish a national water infrastructure research, development, and demonstration program and regional university water research centers; and (3) take back and dispose of prescription and over-the-counter drugs in an environmentally sound manner.