Water Quality Investment Act of 2009

Water Quality Investment Act of 2009 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to: (1) repeal the requirement that the Administrator of the Environmental Protection Agency (EPA) have a specified amount available for grants to states for establishing water pollution control revolving funds in order to make sewer overflow control grants; and (2) require projects receiving sewer overflow control grant assistance to be carried out subject to the requirements applicable to projects receiving assistance from state water pollution control revolving funds, except to the extent that the governor of the state in which the project is located determines that a revolving fund requirement is inconsistent with the purposes of the sewer overflow control grant program.

Authorizes appropriations for sewer overflow control grants for FY2010-FY2014 and sets forth provisions governing the allocation of such funds to states and munipalities.

Establishes a December 31, 2010, deadline for the Administrator's report to Congress on recommended funding levels for sewer overflow control grants.