(This measure has not been amended since it was introduced in the House on February 13, 2003. The summary of that version is repeated here.)Wastewater Treatment Works Security Act of 2003 - Amends the Federal Water Pollution Control Act to authorize the Administrator of the Environmental Protection Agency (EPA) to make grants to a State, municipality, or intermunicipal or interstate agency to conduct a vulnerability assessment of a publicly owned treatment works and implement security enhancements for such facilities upon completion of the assessment. Authorizes the Administrator to: (1) provide technical guidance and assistance to small publicly owned treatment works (those serving a population of fewer than 20,000 persons) on conducting vulnerability assessments and implementing security enhancements; and (2) make grants to a nonprofit organization to improve vulnerability self-assessment methodologies and tools for publicly owned treatment works, including those that are part of a combined wastewater treatment and water supply system. Authorizes appropriations.