In this study, a model-referenced underwater navigation algorithm is proposed for high-precise underwater navigation using monocular vision near underwater structures. The main idea of this navigation algorithm is that a 3D model-based pose estimation is combined with the inertial navigation using an extended Kalman filter (EKF). The spatial information obtained from the navigation algorithm is utilized for enabling the underwater robot to navigate near underwater structures whose geometric models are known a priori. For investigating the performance of the proposed approach the model-referenced navigation algorithm was applied to an underwater robot and a set of experiments was carried out in a water tank.