The measurement of the motion of a small-scale wave energy device during wave tank tests is important for the evaluation of its response to waves and the assessment of power production. Usually, the motion of a small-scale wave energy converter (WEC) is measured using an optical motion tracking system with high precision and sampling rate. However, the cost for an optical motion tracking system can be considerably high and, therefore, the overall cost for tank testing is increased. This paper proposes a low-cost capture system composed of an inertial measurement unit and ultrasound sensors. The measurements from the ultrasound sensors are combined optimally with the measurements from the inertial measurement unit through an extended Kalman filter (EKF) in order to obtain an accurate estimation of the motion of a WEC.