This paper details the development of an autonomous motion-control and navigation algorithm for an underwater autonomous vehicle, the Ocean Server IVER3, to track long linear features such as underwater pipelines. As part of this work, the Nonlinear and Autonomous Systems Laboratory (NAS Lab) developed an algorithm that utilizes inputs from the vehicles state of the art sensor package, which includes digital imaging, digital 3-D Sidescan Sonar, and Acoustic Doppler Current Profilers. The resulting algorithms should tolerate real-world waterway with episodic strong currents, low visibility, high sediment content, and a variety of small and large vessel traffic.