We present an efficient computational algorithm for estimating the noise covariance matrices of large linear discrete stochasticdynamic systems. Such systems arise typically by discretizing distributed-parameter systems, and their size renders computational efficiency a major consideration. Our adaptive filtering algorithm is based on the ideas of Bélanger, and is algebraically equivalent to his algorithm. The earlier algorithm, however, has computational complexity proportional to p
6, where

is the number of observations of the system state, while the new algorithm has complexity proportional to only p
3. Furthermore, our formulation of noise covariance estimation as a secondary filter, analogous to state estimation as a primary filter, suggests several generalizations of the earlier algorithm. The performance of the proposed algorithm is demonstrated for a distributed system arising in numerical weather prediction.