A new approach in the application of modern system identification and estimation techniques is proposed to help nuclear reprocessing facilities meet the nuclear accountability requirement proposed by the International Atomic Energy Agency. The proposed identification and estimation method considers the material inventory in a portion of the chemical separations area of a reprocessing facility. The method addresses the nonlinear aspects of the problem, the time delay through the separation facility, and the lack of measurement access. The method utilizes only input-output measured data and knowledge of the uncertainties associated with the process and measured data. The approach of accurate materials accountability presented could also be applied to other processes exhibiting the same characteristics such as time delays, nonlinear process, and the lack of measurement access.