This paper proposes methods to enable autonomous operation, specifically for localization and motion planning, of net grooming robots in aquaculture net pens and validates the proposed methods in both simulations and experimental fieldwork. Moreover, this paper suggests enabling uninterrupted operation by investigating the use of data from an inertial measurements unit that is a common sensor in underwater vehicles, rather than investing and upgrading to costly sensory systems that often require additional installation and calibration. In particular, the presented work consists of a localization method capable of estimating a robotic system's cylindrical position in an aquaculture net pen, a 3~DOF cylindrical robotic model, a method for path planning and collision avoidance, and a heading guidance and control system. The simulations demonstrate successful localization of the robotic system, while simultaneously planning and following collision-free trajectories in an environment obstructed by obstacles. Furthermore, the field trials successfully demonstrate that the system, when applied to net crawling robots, is capable of localization, path planning, and collision avoidance in an aquaculture setting. As follows, the presented work contributes to establishing net grooming robots as competitive candidates for biofouling management.