Water Protection and Reinvestment Act of 2012

Water Protection and Reinvestment Act of 2012 - Amends the Internal Revenue Code to establish the Water Protection and Reinvestment Trust Fund to support investments in clean water infrastructure. Imposes through 2019 an excise tax on the sale of containers of water-based beverages, water disposal products, and pharmaceutical products and appropriates revenues raised from such taxes to the Trust Fund.

Requires the Director of the Congressional Budget Office (CBO) to study and report on potential funding mechanisms and revenue sources for a clean water trust fund.

Directs the Administrator of the Environmental Protection Agency (EPA) to allocate amounts from the Trust Fund for specified clean water programs, specified grants under the Federal Water Pollution Control Act (commonly known as the Clean Water Act), and other specified activities under this Act.

Amends the Clean 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 Act.

Authorizes the Administrator to use Trust Fund amounts: (1) to make grants to ensure the adequate supply of certified wastewater treatment operators, (2) to award scholarships for undergraduate and graduate study by persons who plan to enter an occupation involving the operation and maintenance of treatment works, and (3) for sewer overflow control grants.

Requires the Administrator to: (1) establish a national water infrastructure research, development, and demonstration program to develop, demonstrate, and transfer innovative or improved technologies and methods for the treatment, control, transport, and reuse of wastewater; (2) make grants to nonprofit institutions of higher learning to establish and operate one university water research center in each of such 21 hydro-regions and designate one of such centers as the National Water Research Center; (3) enter an arrangement for a National Academy of Sciences study of the means by which public water systems meet the costs associated with operations, maintenance, capital replacement, and regulatory requirements; and (4) establish a program of grants to local and state entities to reduce discharges of harmful pollutants into navigable waters through programs to take back prescription and over-the-counter drugs from the public and dispose of them in an environmentally sound manner.

Directs the Secretary of the Treasury to: (1) establish an education program to inform the public about clean water benefits associated with taxes paid to the Trust Fund, and (2) carry out an innovative financing program to make financial assistance available for projects eligible for funding under water pollution control revolving loan funds.