This paper presents an online technique which employs incremental support vector regression to learn the damping term of an underwater vehicle motion model, subject to dynamical changes in the vehicle's body. To learn the damping term, we use data collected from the robot's on-board navigation sensors and actuator encoders. We introduce a new sample-efficient methodology which accounts for adding new training samples, removing old samples, and outlier rejection. The proposed method is tested in a real-world experimental scenario to account for the model's dynamical changes due to a change in the vehicle's geometrical shape.