This bill amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to authorize the Environmental Protection Agency's Great Lakes Restoration Initiative for FY2016-FY2020.

The Initiative must prioritize and carry out programs and projects for Great Lakes protection and restoration, including: (1) the remediation of toxic substances and areas of concern; (2) the prevention and control of invasive species and their impacts; (3) the protection and restoration of near-shore health and the prevention and mitigation of nonpoint source pollution (water pollution that comes from many diffuse sources, such as pollution on the ground picked up by rain or snow); and (4) habitat and wildlife protection and restoration.

Funding made available to implement the Initiative may not be used for any water infrastructure activity (other than a green infrastructure project that improves habitat and other ecosystem functions in the Great Lakes) for which funding is made available under the clean water or drinking water state revolving fund program.

Federal agencies must maintain the base level of funding for their Great Lakes activities without regard to funding under the Initiative and identify new activities to support the environmental goals of the Initiative.

(Sec. 2) This bill amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to revise and reauthorize the Environmental Protection Agency's (EPA) Great Lakes Restoration Initiative for FY2017-FY2021.

The bill restates the initiative's priorities for Great Lakes protection and restoration programs and projects, including: (1) the remediation of toxic substances and areas of concern; (2) the prevention and control of invasive species and their impacts; (3) the protection and restoration of near-shore health and the prevention and mitigation of nonpoint source pollution (water pollution that comes from many diffuse sources, such as pollution on the ground picked up by rain or snow); (4) habitat and wildlife protection and restoration; and (5) accountability, monitoring, evaluation, communication, and partnership activities.

In selecting the best combination of the initiative's programs and projects, the EPA must consult with the Great Lake states and Indian Tribes and solicit input from other non-federal stakeholders.

The EPA must designate a point person from an appropriate federal partner to coordinate, with federal partners and non-federal stakeholders, the initiative's projects and activities involving harmful algal blooms in the Great Lakes.

In addition to current requirements concerning the use of funds made available to carry out the initiative, the bill requires initiative funds to be used to strategically implement operations and activities of EPA's Great Lakes National Program Office, such as remediation of sediment contamination in areas of concern.

The EPA or federal department or agency that receives funds under the initiative may make a grant to, or enter into an agreement with, a qualified nonfederal entity for planning, researching, monitoring, outreach, or implementation of a project that supports the Initiative Action Plan or the Great Lakes Water Quality Agreement.

Projects may be carried out under the initiative on multiple levels, including at the local level.

Funding made available to implement the initiative may not be used for any water infrastructure activity (other than a green infrastructure project that improves habitat and other ecosystem functions in the Great Lakes) for which funding is made available under the Water Infrastructure Finance and Innovation Act of 2014.

The EPA must review, and revise if appropriate, the Initiative Action Plan at least once every five years. The EPA must also: (1) establish a process for monitoring and periodically reporting to the public on the plan's progress, (2) make information about each project carried out under the plan available on a public website, and (3) provide to specified congressional committees a yearly detailed description of the initiative's progress and amounts transferred to participating federal departments and agencies for carry out activities that support the initiative.

Great Lakes Restoration Initiative Act of 2016

(Sec. 2) This bill amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to revise and reauthorize the Environmental Protection Agency's (EPA) Great Lakes Restoration Initiative for FY2017-FY2021.

The bill restates the initiative's priorities for Great Lakes protection and restoration programs and projects, including: (1) the remediation of toxic substances and areas of concern; (2) the prevention and control of invasive species and their impacts; (3) the protection and restoration of near-shore health and the prevention and mitigation of nonpoint source pollution (water pollution that comes from many diffuse sources, such as pollution on the ground picked up by rain or snow); (4) habitat and wildlife protection and restoration; and (5) accountability, monitoring, evaluation, communication, and partnership activities.

In selecting the best combination of the initiative's programs and projects, the EPA must consult with the Great Lake states and Indian Tribes and solicit input from other non-federal stakeholders.

The EPA must designate a point person from an appropriate federal partner to coordinate, with federal partners and non-federal stakeholders, the initiative's projects and activities involving harmful algal blooms in the Great Lakes.

In addition to current requirements concerning the use of funds made available to carry out the initiative, the bill requires initiative funds to be used to strategically implement operations and activities of EPA's Great Lakes National Program Office, such as remediation of sediment contamination in areas of concern.

The EPA or federal department or agency that receives funds under the initiative may make a grant to, or enter into an agreement with, a qualified nonfederal entity for planning, researching, monitoring, outreach, or implementation of a project that supports the Initiative Action Plan or the Great Lakes Water Quality Agreement.

Projects may be carried out under the initiative on multiple levels, including at the local level.

Funding made available to implement the initiative may not be used for any water infrastructure activity (other than a green infrastructure project that improves habitat and other ecosystem functions in the Great Lakes) for which funding is made available under the Water Infrastructure Finance and Innovation Act of 2014.

The EPA must review, and revise, if appropriate, the Initiative Action Plan at least once every five years. The EPA must also: (1) establish a process for monitoring and periodically reporting to the public on the plan's progress, (2) make information about each project carried out under the plan available on a public website, and (3) provide to specified congressional committees a yearly detailed description of the initiative's progress and amounts transferred to participating federal departments and agencies for carrying out activities that support the initiative.