The hydraulic turbocharger plays a vital role in harnessing the energy stored in brine within reverse osmosis desalination plants. To optimize the efficiency and durability of this equipment, it is crucial to develop accurate dynamic models of the turbocharger rotor. An improved understanding of rotor dynamics enables the integration of innovative technologies such as Hydraulic Energy Management Integration, effectively enhancing efficiencies in systems characterized by small capacities and high rotational speeds. This study presents a dynamic modeling methodology for the hydraulic turbocharger. The analysis involves approximating the turbocharger rotor with an equivalent finite element shaft line model. Verification of the model’s natural frequency is conducted using three-dimensional finite element analysis, employing the ANSYS modal analysis module. Computational fluid dynamics is employed to evaluate the fluid forces, while the Reynolds equation is utilized to assess the journal bearing forces. The resulting model is employed to investigate the nonlinear dynamics of the rotor, examining the impact of various system parameters, including rotational speed, unbalance forces, and shaft geometrical parameters. The results highlight the significance of balancing the turbine and pump disks for optimal performance. Furthermore, the research demonstrates that increasing the shaft length reduces the rotor’s threshold speed, while increasing the shaft diameter initially raises the threshold speed until it reaches a critical value. Beyond this critical value, further increases in shaft diameter lead to a decrease in the threshold speed.