The main purpose of this study is to reveal the coupling relationship between rotor nonlinear dynamics (ND) and mixed thermal-visco-hyperelastic hydrodynamic lubrication (MTVHHL) in water-lubricated rubber bearings (WLRBs), referred to as ND-MTVHHL performance for simplicity. To achieve this, a comprehensive mathematical model is developed by integrating a rotor ND model with a transient MTVHHL model of WLRBs. To validate the proposed model, a tribo-dynamic experiment on a WLRB is conducted, and the measured average friction coefficient and transient rotor displacements are compared with numerical predictions of the model. Based on the numerical model, the effects of key rubber parameters—including relaxation time and characteristic scale coefficient—as well as the influence of the underwater environment on transient ND-MTVHHL performance are systematically investigated. It is found that increasing either the average relaxation time or the characteristic scale coefficient reduces the journal trajectory range, while both lead to higher transient viscoelastic contact forces at the rubber-journal interface. Furthermore, transient viscoelastic dissipation is identified as the primary contributor to the time-varying total friction coefficient and heat flux. Finally, the numerical results indicate that both increased seawater pressure and temperature result in a rise in transient contact force, while elevated seawater pressure contributes to reduced journal stability.