Effective monitoring of ship and port basin is essential for optimizing the marine operations, ensuring the safety and protecting the port environment. However, the existing monitoring approaches still have the problems of low intelligence, high cost and poor reliability. This chapter attempts to employ MUSs to develop a ubiquitous monitoring system for ship and port basin. Particularly, it mainly includes two AUVs, a human operator, two onshore cameras, and a wireless communication network. With the wireless communication network, human operator in control center sends its monitoring task to AUVs and onshore cameras. After that, the cameras mounted on AUVs and shore collect the ship waterline images, such that the ship attitudes can be estimated by using deep learning technology. In order to ensure the safety of ship navigation and port facilities, sonars are mounted on AUVs to carry out water depth detection and port wall inspection. Finally, experimental results are provided to verify the effectiveness of our system. These results provide evidence that the AUV-assisted monitoring system can improve the reliability and reduce the cost over the manual monitoring system.