Great Lakes Nutrient Removal Assistance Act - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to require the Administrator of the Environmental Protection Agency (EPA) to establish a program to provide grants to Illinois, Indiana, Michigan, Minnesota, New York, Ohio, Pennsylvania, and Wisconsin and municipalities in such states to upgrade eligible municipal wastewater treatment plants with nutrient removal technologies. Requires the Administrator to give priority to plants at which nutrient removal technology upgrades would: (1) produce the greatest nutrient load reductions at points of discharge, (2) result in the greatest environmental benefits to the Great Lakes System, and (3) help meet the objectives related to nutrients outlined in Annex four of the 2012 Great Lakes Water Quality Agreement.

Defines as "eligible" a plant that: (1) has a permitted design capacity to treat an annual average of at least 500,000 gallons of wastewater per day, and (2) is located within the Great Lakes System in any of such states.

Prohibits the federal share from exceeding 55% of the total cost of upgrading such plants.