This paper proposes an integrated positioning system to localize a moving object in the shadow-area that exists in the water tank. The new water tank for underwater robots is constructed to evaluate the navigation performance of underwater vehicles. Several sensors are integrated in the water tank to provide the position information of the underwater vehicles. However there are some areas where the vehicle localization becomes very poor since the very limited sensors such as sonar and depth sensors are effective in underwater environment. Also there are many disturbances at sonar data. To reduce these disturbances, an extended Kalman filter has been adopted in this research. To localize the underwater vehicles under the hostile situations, a SVR (Support Vector Regression) has been systematically applied for estimating the position stochastically. To demonstrate the performance of the proposed algorithm (an extended Kalman filter + SVR analysis), a new UI (User Interface) has been developed.