Reducing the carbon emissions of ships and increasing the utilization of marine renewable energy are the important ways to achieve the goal of carbon neutrality in ocean engineering. Establishing an accurate mathematical model is the foundation of simulating the motion of marine vehicles and structures, and it is the basis of operation energy efficiency optimization and prediction of power generation. System identification from observed input–output data is a practical and powerful method. However, for modeling objects with different characteristics and known information, a single modeling framework can hardly meet the requirements of model establishment. Moreover, there are some challenges in system identification, such as parameter drift and overfitting. In this work, three robust methods are proposed for generating ocean hydrodynamic models based on Bayesian regression. Two Bayesian techniques, semi-conjugate linear regression and noisy input Gaussian process regression are used for parametric and nonparametric gray-box modeling and black-box modeling. The experimental free-running tests of the KRISO very large crude oil carrier (KVLCC2) ship model and a multi-freedom wave energy converter (WEC) are used to validate the proposed Bayesian models. The results demonstrate that the proposed schemes for system identification of the ship and WEC have good generalization ability and robustness. Finally, the developed modeling methods are evaluated considering the aspects required conditions, operating characteristics, and prediction accuracy.