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

Authorizes funding to be provided through cooperative agreements, grants, or other means to state and local agencies, special districts, public or nonprofit agencies, institutions, and organizations. Prohibits funding from being used for the administration of a management conference for the San Francisco estuary under the National Estuary Program.

Requires the Administrator, in developing the priority list, to consult with and consider the recommendations of: (1) the San Francisco Estuary Partnership, (2) the state of 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 funding amounts under this Act to 75% of the total cost of eligible activities to be carried out using those amounts.

Authorizes the Administrator to carry out this Act for each of FY2013-FY2017.