This paper presents a filter for underwater positioning in an aquaculture environment with demanding weather conditions. The positioning system is based on acoustic transponders mounted at a net pen on the sea surface. The transponders are exposed to oscillations due to wave disturbance. This will have an impact on the accuracy of the positioning system. An extended Kalman filter (EKF) solution has been proposed including a wave motion model integrated with the pseudo-range measurements from the transponders. Simulations show that the proposed filter compensates well for the disturbances.

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