The authors of the paper propose an approach to the control of the underwater vehicles, the mathematical model of which is known with a certain degree of accuracy, namely, its linear part. The proposed approach is based on the use of the estimates of the phase coordinate of the control object, and the estimates of the unknown external disturbances, which represent a collection of the external influences, and incomplete information about the model of the control object. The authors of this paper propose the filtering algorithms, based on separation of the residuals of the high and low frequency components and allow us to recover not only the phase coordinates of the movement, but the unknown perturbations. The paper also offers control algorithms for the underwater vehicles based on the use of not only estimates of the movement coordinates, but also the estimates of the unknown disturbances, obtained due to the filtering algorithms. Compared with the classical control laws, these algorithms allow us to significantly improve the quality control of the modern underwater vehicles. The paper contains a smoothing algorithm of the signal applied to the controller. This can significantly reduce the load on the governing bodies and thereby improve their performance. Conducted on the example of a non-planar motion of an underwater vehicle described by a complex system of nonlinear differential equations under the action of a slowly varying wave disturbances and modeling, the experiments confirm RA-combat capability proposed in the paper algorithms for filtering and control.