An ultra-short baseline (USBL) system and a Doppler Velocity Log (DVL) system, both commonly applied for navigation and guidance of underwater vehicles, were tested with respect to their capabilities to support aquaculture net pen inspection by remote-operated-vehicles (ROVs). The data from these systems were investigated with respect to this new application and its operational demands. A series of full scale experiments indicate that the DVL system is able to detect sea pen nets equally well as the seabed, and the USBL system is able to transmit through a net pen containing industrial-scale biomass. A navigation system that uses a combination of these instruments will report the position of the ROV relatively to the net pen, and enable proper documentation of the traveled path. By equipping a suitable underwater vehicle with a combination of USBL and DVL technology, autonomous net inspections with reliable coverage can be achieved. Such a system would have considerable potential for remote and offshore aquaculture farming systems.