In this paper, an output-feedback fuzzy adaptive dynamic surface controller (FADSC) based on fuzzy adaptive extended state observer (FAESO) is proposed for autonomous underwater vehicle (AUV) systems in the presence of external disturbances, parameter uncertainties, measurement noises and actuator faults. The fuzzy logic system is incorporated into both the observers and controllers to improve the adaptability of the entire system. The dynamics of the AUV system is established first, considering the external disturbances and parameter uncertainties. Based on the dynamic models, the ESO, combined with a fuzzy logic system tuning the observer bandwidth, is developed to not only adaptively estimate both system states and the lumped disturbances for the controller, but also reduce the impact of measurement noises. Then, the DSC, together with fuzzy logic system tuning the time constant of the low-pass filter, is designed using estimations from the FAESO for the AUV system. The asymptotic stability of the entire system is analyzed through Lyapunov’s direct method in the time domain. Comparative simulations are implemented to verify the effectiveness and advantages of the proposed method compared with other observers and controllers considering external disturbances, parameter uncertainties and measurement noises and even the actuator faults that are not considered in the design process. The results show that the proposed method outperforms others in terms of tracking accuracy, robustness and energy consumption.