M. Tech. (Department of Mechanical Engineering, Faculty of Engineering and Technology), Vaal University of Technology. / Fault diagnosis of a rotor system operating in a fluid is one of the most difficult aspects of rotating machinery. Fluid in machinery plays a significant role in concealing the allowable rubbing stress limit during the impact generated from the rotor-stator rub which may progressively deteriorate the rotating system. Therefore, a numerical and experimental investigation was performed to analyse the influence of the fluid during the rotor-stator contact of a vertical rotor system partially submerged in an incompressible inviscid fluid with a focus on detecting rubbing fault in the presence of axial load. The theoretical model of lateral-torsional rotor consists of a 3-D rub-impact induced parametric excitation, which was assimilated to operate as elastic vertical rotor system by considering the transient vibration of a flexible axial force and energy of the vertical shaft system. The model was established based on Jeffcott rotor, time-varying stiffness and the rotor-stator fluid interaction. The Lagrangian principle was used to establish the governing equation of motion. The hydrodynamic forces acting on the vertical rotor were established and introduced into the system based on the Laplace form of the linearized Navier–Stokes equations under lateral excitation yielding a highly nonlinear 5-DOF system. To evaluate the dynamic response and ensure the accurate acquisition of rubbing features in a fluid, the classical Fast Fourier Transform (FFT) and the vibration waveform have been discretised and illustrated through the frequency components. Furthermore, for effective extraction of some hidden features of rub, the nonlinear features embedded in the vibration waveform have been discretised and illustrated through to the lateral deformation of the rotor and the orbit patterns of the shaft. Qualitative numerical analysis suitable for highly nonlinear and non-stationary signal Time-Frequency strategies, Wavelet Synchrosqueezed Transform (WSST) and Instantaneous Frequency (IF) technique were employed to successfully extract the frequency of oscillating modes and the periodic frequency response of the faulted rotor system. It is demonstrated that the coupled lateral-torsional vibration of the submerged vertical rotor system has the potential to enhance the much-unwanted hidden frequencies of vibration that leads to significant instability of the rotor system. In particular, the responses revealed the existence of unstable regimes with respect to the lateral-torsional deflection as well as the angular velocity. High harmonic peaks were also identified at the critical speed, which can be considered as a monitoring index to detect the rubbing in rotating shafts in a fluid. It was found that even at relatively slow rotating speed fluid elastic forces induced by the co-rotating flow surrounding the shaft significantly affect the transverse natural modes of vibration of the shaft. Despite the interaction between the fluid and the rotor generates self-excitation of low frequencies, obtained results indicated that the fluid-rotor interaction reduces the dynamic vibration response of the faulted system running below the second critical speed. It has been analytically demonstrated that the time-varying stiffness induced is the principal cause of the frequency-modification feature of the dynamic response of an unbalance-rub rotor system at the contact region. The model investigated in this study has potential application for drill string-borehole shaft system used in the oil industry.