The increasing ecological awareness and stringent requirements for environmental protection have led to the development of water lubricated journal bearings. For the investigation of water-lubricated journal bearings, a new structured mesh movement algorithm for the CFD model is developed and based on this method, the nonlinear transient hydrodynamic force model is established. Then, with consideration of velocity perturbation, a method to determine dynamic coefficients and linear hydrodynamic forces is promoted. After validation of static equilibrium position and stiffness coefficients, a comparative linear and nonlinear hydrodynamic force analysis of multiple grooves water-lubricated journal bearings (MGWJBs) is conducted. The calculation results indicate that the structured mesh movement algorithm is suitable for the dynamic characteristics investigation of water-lubricated journal bearings. And the comparative study shows that there is a considerable difference between the linear and nonlinear hydrodynamic forces of MGWJBs. Further investigation should be carried to evaluate the dynamic responses of rotor supported by MGWJBs under difference force models.