Experiments in ground-test facilities are required to develop and mature aero-optic platforms. However, structural vibrations of the facility can introduce significant error in optical experiments, making it difficult to separate wind tunnel dynamics from the aero-optic measurements of interest. As a means of performing this separation, a Kalman filtering scheme, tuned using the Autocovariance Least-Squares method, is implemented to measure the dynamic motion of a generalized aero-optic model geometry. An example is presented for the case of a laser diode mounted on a flexible post undergoing vibration. Using a single three-axis accelerometer, combined with a priori knowledge of the system’s structural dynamics, pitch angle fluctuations on the order of 0.01 degree were successfully estimated within 0.002 degree uncertainty.