Abstract : The complexity of the laws of dynamics governing 3-D atmospheric flows associated with incomplete and noisy observations make the recovery of atmospheric dynamics from satellite image sequences very difficult. In this paper, we address the challenging problem of estimating physical sound and time-consistent horizontal motion fields at various atmospheric depths for a whole image sequence. Based on a vertical decomposition of the atmosphere, we propose a dynamically consistent atmospheric motion estimator relying on a multilayer dynamic model. This estimator is based on a weak constraint variational data assimilation scheme and is applied on noisy and incomplete pressure difference observations derived from satellite images. The dynamic model is a simplified vorticity-divergence form of a multilayer shallow-water model. Average horizontal motion fields are estimated for each layer. The performance of the proposed technique is assessed using synthetic examples and using real world meteorological satellite image sequences. In particular, it is shown that the estimator enables exploiting fine spatio-temporal image structures and succeeds in characterizing motion at small spatial scales.