By the use of IoT, Waterborne Transportation Systems (WTSs) have significantly advanced in recent years. With improved communication services and added features like caching, processing, monitoring and managing a broad range of IoT gadgets, the advent of 6G cellular networks has additionally increased potentials. In spite of these technological advances, new safety and reliability issues and challenges have been brought about by the convergence of IoT and 6G. This paper provides an authentication framework (AF), specifically developed for 6G-IoT-enabled WTS. The main objective is to manage real-time data by utilizing decentralized cloud servers that are peer-to-peer, while also considering the security and privacy requirements of WTS. Additionally, this connection helps to reduce a variety of security risks. Thorough assessment by Scyther tool and informal security study, confirms the privacy and security of the protocol. Also its security features and computational costs in comparison to current protocols, showing that it is more secure and efficient.