To enhance homeland security in the ports and waterways of the United States, and for other purposes.

America's Waterway Watch Act - Establishes within the Coast Guard the America's Waterway Watch Program to promote voluntary reporting of activities indicating a threat or act of terrorism against a vessel, facility, port, or waterway.

Requires the Secretary of Homeland Security (DHS) to: (1) report to specified congressional committees and to the Comptroller General on the pilot program to test the business processes, technology, and operational impacts required to deploy transportation security card readers at secure areas of the marine transportation system; (2) report to specified congressional committees on the establishment of Interagency Operational Centers for Port Security and on the threat, vulnerability, and consequence of a terrorist attack on gasoline and chemical cargo shipments in port activity areas; (3) establish no less than two maritime security response teams to act as the Coast Guard's counterterrorism and law enforcement response units; (4) increase the number of detection canine teams certified by the Coast Guard for maritime-related security; (5) conduct a program for the mobile biometric identification of suspected individuals, including terrorists, to enhance border security; (6) establish a pilot program to test and deploy preventive radiological or nuclear detection equipment on Coast Guard vessels to enhance border security; (7) establish procedures for fingerprinting applicants for transportation security cards and prepare an assessment of the enrollment sites for such cards; and (8) initiate a national study to identify measures for improving the security of maritime transportation of certain dangerous cargo and coordinate an evaluation of the waterside security of vessels carrying, and waterfront facilities handling, certain dangerous cargo.

Directs the Comptroller General to: (1) study the effects that the Transportation Worker Identification Credential (TWIC) has on companies that employ seasonal employees; (2) study methods to conduct a background security investigation of an individual who possesses a biometric identification card that complies with International Labor Convention number 185; and (3) report to specified congressional committees regarding background checks and forms of identification required under state and local transportation security programs.

Requires the Commandant of the Coast Guard to promote maritime security and ensure appropriate coverage of maritime security missions within the workforce. Authorizes the Commandant to establish and operate one or more centers of expertise for maritime security.