The mesosphere and lower thermosphere (MLT) are regions that absorb and modify atmospheric phenomena originating in the troposphere and stratosphere. However, these are also source regions for dynamical, chemical and radiative processes that act to redistribute energy and constituents throughout the upper atmosphere. The MLT is monitored by the Upper Atmosphere Research Satellite (UARS) and the Thermosphere-Ionosphere-Mesosphere Dynamics and Energetics (TIMED) spacecraft, as well as ground-based networks of lidars, optical sensors, and medium frequency (MF) and meteor wind (MW) radars. In support of the TIMED mission science goals, and their application to the Space Weather Program, we have developed a sequential estimator for the assimilation of ground- and satellite-based MLT wind measurements. Preliminary experiments have focused on the retrieval of monochromatic waves sampled by the TIMED satellite and MF observing network. Ground-based measurements are found to be a critical compliment to the satellite database for defining the variability of tides. The sequential estimator is currently being tested on output from the NCAR Whole Atmosphere Community Climate Model (WACCM).