This paper presents an uncalibrated visual servoing scheme for underwater vehicle manipulator systems (UVMSs) with an eye-in-hand camera under uncertainties. These uncertainties contain vision sensor parameters, UVMS kinematics and feature position information. At first, a linear separation approach is addressed to collect these uncertainties into vectors, and this approach can also be utilized in other free-floating based manipulator systems. Secondly, a novel nonlinear adaptive controller is proposed to achieve image error convergence by estimating these vectors, the gradient projection method is utilized to optimize the restoring moments. Thirdly, a high order disturbance observer is addressed to deal with time-varying disturbances, and the convergence of the image errors is proved under the Lyapunov theory. Finally, in order to illustrate the effectiveness of the proposed method, numerical simulations based on a 9 degrees of freedom (DOFs) UVMS with an eye-in-hand camera are conducted. In simulations, the UVMS is expected to track a circle trajectory on the image plane, meanwhile, time-varying disturbances are exerted on the system. The proposed scheme can achieve accurate and smooth tracking results during simulations.