Water Quality Protection and Job Creation Act of 2011

Water Quality Protection and Job Creation Act of 2011 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act [CWA]) to authorize the Administrator of the Environmental Protection Agency (EPA) to make grants to nonprofit organizations to provide: (1) technical assistance to rural and small municipalities and tribal governments for planning, developing, and financing eligible state water pollution control revolving fund projects; and (2) technical assistance and training to enable rural, small, and tribal publicly owned treatment works and decentralized wastewater systems to protect water quality and comply with the CWA.

Authorizes annual appropriations for FY2012-FY2016 for: (1) grants to states for administering programs for the prevention, reduction, and elimination of pollution; (2) watershed pilot projects (currently called wet weather watershed pilot projects); (3) grants to states for water pollution control revolving funds; (4) a pilot program for alternative water source projects; and (5) sewer overflow control grants.

Expands the types of watershed pilot projects eligible for technical assistance and grants. Revises: (1) the eligibility requirements for grants for sewage collection systems; and (2) provisions concerning state water pollution control revolving funds, including by expanding the types of projects eligible for assistance. Requires states to: (1) establish affordability criteria to identify municipalities that would experience a significant hardship raising revenue for state water pollution control revolving fund projects, (2) establish a list of such projects that prioritizes water quality improvement projects for FY2013 and thereafter, and (3) provide financial assistance to only projects on such list.

Requires the Administrator to report annually on the performance of the projects and activities carried out with assistance made available by a state water pollution control revolving fund.

Prohibits state water pollution control revolving funds from being used for a project for the construction of publicly owned treatment works unless the steel, iron, and manufactured goods used in such project are produced in the United States, with specified exceptions. Requires the Administrator to prohibit the use of steel, iron, and manufactured goods produced in a foreign country in a project funded with amounts made available from such fund if such country is in violation of the terms of an agreement with the United States by discriminating against such goods that are produced in the United States.

Authorizes the Administrator to waive the requirement that a state deposit an amount equal to 20% of the state's annual capitalization grant into the state's water pollution control revolving fund if the Administrator determines that the state is experiencing economic hardship and that providing such a deposit would adversely impact the state's ability to restore and maintain the chemical, physical, and biological integrity of its waters.

Revises provisions concerning: (1) state water pollution control revolving fund amounts reserved for Indian tribes, and (2) the use of such amounts.

Changes the tonnage duty (currently, a tax) on specified vessels entering or returning to a U.S. port.

Amends the Internal Revenue Code to establish the Clean Water Trust Fund for: (1) capitalization grants to states for water pollution control revolving funds; (2) grants to states for water pollution control programs; (3) grants for research for the prevention, reduction, and elimination of water pollution; and (4) direct loans or guaranteeing obligations authorized under provisions of this Act entitled the Water Pollution Control Investment Act.

Water Pollution Control Investment Act - Authorizes the Administrator to: (1) make a direct loan to a state infrastructure financing authority for use in the same manner as a capitalization grant made under the CWA for state water pollution control revolving funds, and (2) guarantee obligations for construction of large water infrastructure projects.