Wastewater Treatment Works Security Act of 2009

Wastewater Treatment Works Security Act of 2009 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to require each owner or operator of a treatment works that stores or uses a substance of concern in quantities deemed by the Administrator of the Environmental Protection Agency (EPA) to pose a security risk to conduct a vulnerability assessment of its treatment works, which shall include a site security plan to identify specific security enhancements.

Directs the Administrator to develop and publish guidelines for carrying out a vulnerability assessment and, in developing such guidelines, to: (1) develop standards for assigning individual treatment works to four risk-based classifications taking into consideration a works' size and proximity to large population centers and the potential impacts of intentional acts on public health or safety or the environment; (2) designate any chemical substance as a substance of concern; and (3) include a process for the revision, resubmission, and review of vulnerability assessments. Directs the Administrator to establish a threshold quantity for the release or theft of each such substance. Sets forth requirements and deadlines for assessment certification, submission, review, approval, and disclosure.

Authorizes the Administrator to make grants to a state, municipality, or intermunicipal or interstate agency to conduct a vulnerability assessment of a publicly owned treatment works, to implement specified security enhancements to reduce identified vulnerabilities, and to provide for security-related training of treatment works employees and training for emergency response providers.

Authorizes the Administrator: (1) in coordination with the states, to provide technical guidance and assistance to small publicly owned treatment works on conducting a vulnerability assessment and implementation of security enhancements; and (2) to make grants to nonprofit organizations to assist in accomplishing purposes of this Act.