Unmanned Underwater Vehicles (UUVs) are widely used in commercial, scientific, and military missions for various purposes. What makes this technology challenging is the increasing mission duration and unknown environment. It is necessary to embed fault-tolerant control paradigms into UUVs to increase the reliability of the vehicles and enable them to execute and finalize complex missions. Specifically, fault-tolerant control (FTC) comprises fault detection, identification, and control reconfiguration for fault compensation. Literature review shows that there have been no systematic methods for fault-tolerant control of UUVs in earlier investigations. This study presents a hierarchical methodology of fault detection, identification and compensation (HFDIC) that integrates these functions systematically in different levels. The method uses adaptive finite-impulse-response (FIR) modeling and analysis in its first level to detect failure occurrences. Specifically, it incorporates a FIR filter for on-line adaptive modeling, and a least-mean-squares (LMS) algorithm to minimize the output error between the monitored system and the filter in the modeling process. By analyzing the resulting adaptive filter coefficients, we extract the information on the fault occurrence. The HFDIC also includes a two-stage design of parallel Kalman filters in levels two and three for fault identification using the multiple-model adaptive estimation (MMAE). The algorithm activates latter levels only when the failure is detected, and can return back to the monitoring loop in case of false failures. On the basis of MMAE, we use multiple sliding-mode controllers and reconfigure the control law with a probability-weighted average of all the elemental control signals, in order to compensate for the fault. We validate the HFDIC on the steering and diving subsystems of Naval Postgraduate School (NPS) UUVs for various simulated actuator and/or sensor failures, and test the hierarchical fault detection and identification (HFDI) with realistic data from at-sea experiment of the Florida Atlantic University (FAU) Autonomous Underwater Vehicles (AUVs). For both occasions, we model actuator and sensor failures as additive parameter changes in the observation matrix and the output equation, respectively. Simulation results demonstrate the ability of the HFDIC to detect failures in real time, identify failures accurately with a low computational overhead, and compensate actuator and sensor failures with control reconfiguration. In particular, verification of HFDI with FAU data confirms the performance of the fault detection and identification methodology, and provides important information on the vehicle performance. / Ph. D.