Position tracking of an autonomous underwater vehicle is not trivial as its accuracy is affected by process noise, measurement noise, and uncertain hydrodynamic parameters. Thus, in this article, we studied the position control of an autonomous underwater vehicle that operates under largely unbounded system uncertainties and large noise levels and proposed a method that reduces the interference and thereby enhances the overall autonomous underwater vehicle position estimation. Our technique extended the ensemble Kalman filter by combining it with a time-delay estimator to compensate against extended uncertainty of the system dynamics which cannot be solved by the traditional ensemble Kalman filter. Our synthetic simulations demonstrated the effectiveness of the proposed controller, highlighting its appealing position-control accuracy under simultaneous noise and uncertain hydrodynamics parameters. In addition, our simulation results showed that the proposed controller outperforms the conventional time-delay controller by a percentage range of approximately 30.8%–92.6% in terms of root-mean-square error and requires on average less than 88.2% calculation time than the conventional model predictive control.