San Francisco Bay Restoration Act

San Francisco Bay Restoration Act - 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, or projects identified in an annual priority list, including restoration projects and habitat improvement for fish, waterfowl, and wildlife, that advance the goals and objectives of the comprehensive management plan for the San Francisco Bay estuary.

Requires the Administrator, in developing such list, to consult with and consider the recommendations of: (1) the San Francisco Estuary Partnership, (2) California and affected local governments in the San Francisco Bay estuary watershed, and (3) any other relevant stakeholder involved with the protection and restoration of such estuary.

Limits grant amounts to 75% of the total cost of eligible activities to be carried out using those amounts. Requires the non-federal share of the total cost of any eligible activities to be carried out using amounts provided under this Act to be no less than 25%.

Authorizes appropriations to the Administrator to carry out this Act for each of FY2012-FY2016. Prohibits such amounts from being used by a management conference under the National Estuary Program.