Wastewater Treatment Works Security Act of 2006

Wastewater Treatment Works Security Act of 2006 - (Sec. 2) Amends the Federal Water Pollution Control Act to authorize the Administrator of the Environmental Protection Agency (EPA) to provide grants to any state or local agency or privately owned utility that principally treats municipal wastewater for: (1) a vulnerability assessment of publicly owned treatment works; (2) implementation of security enhancements to reduce identified vulnerabilities; (3) the development, expansion, or upgrading of emergency response plans and site security plans; and (4) the voluntary creation of, or participation in, a mutual aid and emergency network preparedness agreements developed in accordance with the National Incident Management System.

Authorizes the Administrator, upon certification that a vulnerability assessment has been completed and that assistance is sought for a security enhancement, to provide grants for: (1) equipment and activities relating to access control, intrusion prevention and delay, and detection of intruders and hazardous or dangerous substances; (2) an activity to improve security for electronic, computer, or other automated systems and remote security systems; (3) security training; and (4) security screening of employees or contractor support services.

Prohibits: (1) a grant from being used for personnel costs or for the operation or maintenance of facilities, equipment, or systems; and (2) the Administrator from requiring an applicant to provide the Administrator with a copy of a vulnerability assessment, except to view. Provides for the protection of vulnerability assessment information from unauthorized disclosure.

Limits: (1) the federal share of the cost of grant-funded activities for vulnerability assessments and security enhancements to 50%; and (2) the total amount of such grants for publicly owned treatment works to $100,000.

Authorizes the Administrator to: (1) provide technical guidance to small publicly owned treatment works (serving fewer than 10,000 individuals) for a vulnerability assessment, emergency response plan, or site security plan and for implementing security enhancements; and (2) make grants to nonprofit organizations to improve assessment methodologies for publicly owned treatment works and to implement a comprehensive training program for treatment works or privately owned utilities that principally treat municipal wastewater.

(Sec. 3) Requires the Administrator to research and review: (1) means of providing alternative processes to convey, treat, and dispose of wastewater if a disruption of service event occurs; (2) means by which a collection system of a treatment works could be used to convey hazardous substances and secured in response to an intentional harmful act; (3) methods for monitoring a collection system for hazardous substances and unauthorized entry; and (4) treatment technologies.

Authorizes appropriations.