A small-scale experimental setup for autonomous target tracking of a surface vessel in the presence of obstacles is presented. The experiments are performed in simulated rough seas through wave, current, and wind generation in a small indoor pool. Absolute position of the agent and the target as well as the obstacle size and position are provided through an overhead camera by detecting color light emitting diodes installed on all objects. Ordinary differential equations with stable limit-cycle solutions are used to define transitional trajectories around obstacles based on the camera data. A sliding mode control law is implemented for real-time tracking control which is capable of rejecting large disturbances from the generated waves and wind. The sliding mode control signals are sent to wireless receivers on the autonomous vessel where a proportional integral speed controller maintains the commanded speed. A special scaling method is presented to show that the environmental forces are similar to those of moderate through high sea states. Several experiments are presented where the autonomous vessel catches and follows a target boat moving in arbitrary trajectories in both the presence and absence of obstacles.