Which act primarily grants the authority to issue Captain of the Port (COTP) orders regarding vessel security?

The Magnuson Act is the correct choice as it provides the foundation for the authority to issue Captain of the Port (COTP) orders concerning vessel security. This act, officially known as the Magnuson Fishery Conservation and Management Act, includes provisions that empower the COTP to ensure the safety and security of ports and waterways. It allows COTPs to impose necessary regulations and orders that address security threats and breaches in maritime operations, particularly as they relate to ensuring the safety of vessels and protecting the marine environment.

The other options refer to different legislative acts that do not specifically provide the same level of authority regarding vessel security. The Jones Act focuses primarily on the regulation of maritime commerce and the requirements for vessels engaged in domestic trade, while the Port and Waterways Safety Act is primarily concerned with the safety of navigation and infrastructure, and the Clean Water Act is aimed at regulating the discharge of pollutants into U.S. waters rather than security matters. Thus, the Magnuson Act stands out as the key legislative authority for COTPs in the context of vessel security.