In this paper, a fuzzy sliding mode active disturbance rejection control (FSMADRC) scheme is proposed for an autonomous underwater vehicle-manipulator system (AUVMS) with a two-link and three-joint manipulator. First, the AUVMS is separated into nine subsystems, and the combined effects of dynamic uncertainties, hydrodynamic force, unknown disturbances, and nonlinear coupling terms on each subsystem are lumped into a single total disturbance. Next, a linear extended state observer (LESO) is presented to estimate the total disturbance. Then, a sliding mode active disturbance rejection control (SMADRC) scheme is proposed to enhance the robustness of the control system. The stability of the SMADRC and the estimation errors of the LESO are analyzed. Because it is difficult to simultaneously adjust several parameters for a LESO-based SMADRC scheme, a fuzzy logic control (FLC) scheme is used to formulate the FSMADRC to determine the appropriate parameters adaptively for practical applications. Finally, two AUVMS tasks are illustrated to test the trajectory tracking performance of the closed-loop system and its ability to reject and attenuate the total disturbance. The simulation results show that the proposed FSMADRC scheme achieves better performance and consume less energy than conventional PID and FLC techniques.