Although successful applications of data assimilation techniques such as Kalman filter to structural parameter identification problems exist in literature, they have been explored mostly via simulations because real-world application poses challenges. Current practice is to set the process and measurement noise covariance matrices by manual tuning and keeping them constant over the estimation period. However, when the matrices are not correct, Kalman filters are prone to suboptimal performance and/ or even divergence. In this paper, use of a stochastic approximation scheme along with the unscented Kalman filter is explored. The sensitivity of the initial filter parameter selection has been investigated through both simulations and full-scale laboratory experiments. Results show that by automatically updating the filter statistics, system states, including the structural parameters, are successfully estimated with a fast convergence rate, good accuracy, and trackability in a stable and objective manner. The method is further applied to in situ seismic response records of a box-girder bridge. The stiffness values of the rubber bearings are successfully identified.