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This manuscript presents a fully detailed methodology in order to identify the hydrodynamic parameters of a mini autonomous underwater vehicle (mini-AUV) and evaluate its performance using different controllers. The methodology consists of close-to-reality simulation using a Computed Fluid Dynamics (CFD) module of the ANSYS™ Workbench software, the processing of the data, obtained by simulation, with a set of Savistky–Golay filters; and, the application of the Least Square Method in order to estimate the hydrodynamic parameters of the mini-AUV. Finally, these parameters are considered to design the three different controllers that are based on the robot manipulators theory. Numerical simulations are carried out to evaluate the performance of the controllers.