San Francisco Bay Restoration Act of 2011 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to authorize the Administrator of the Environmental Protection Agency (EPA) to provide funding to state and local agencies, special districts, and public or nonprofit agencies, institutions, and organizations for activities, studies, and projects identified in an annual priority list that advance the goals and objectives of the comprehensive conservation and management plan for the San Francisco estuary. Limits funding to 75% of the total cost of eligible activities to be carried out using such funds.
Authorizes appropriations to the Administrator to carry out this Act for each of FY2012-FY2016. Prohibits such funding from being used by a management conference under the National Estuary Program.