Water Quality Investment Act of 2003

Amends the Federal Water Pollution Control Act to 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.

Reauthorizes appropriations for sewer overflow control grants through FY 2010.

Modifies grant funding allocation provisions to reflect new dates of authorization and reauthorized amounts. Eliminates the set-aside for the Administrator of the Environmental Protection Agency to make direct grants to municipalities and municipal entities during the second year of authorization.

Establishes a December 31, 2008, deadline for the Administrator's report to Congress on recommended funding levels for sewer overflow control grants.