In this paper, we address the problem of estimating I mesoscale dynamics of atmospheric layers from satellite image sequences. Due to the great deal of spatial and temporal distortions of cloud patterns and because of the sparse 3-D nature of cloud observations, standard dense-motion field-estimation techniques used in computer vision are not well adapted to satellite images. Relying on a physically sound vertical decomposition of the atmosphere into layers, we propose a dense-motion estimator dedicated to the extraction of multilayer horizontal wind fields. This estimator is expressed as the minimization of a global function including data and spatio-temporal smoothness terms. A robust data term relying on the integrated-continuity equation mass-conservation model is proposed to fit sparse-transmittance observations related to each layer. A novel spatio-temporal smoother derived from large eddy prediction of a shallow-water momentum-conservation model is used to build constraints for large-scale temporal coherence. These constraints are combined in a global smoothing framework with a robust second-order smoother, preserving divergent and vorticity structures of the flow. For optimization, a two-stage motion estimation scheme is proposed to overcome multiresolution limitations when capturing the dynamics of mesoscale structures. This alternative approach relies on the combination of correlation and optical-flow observations in a variational context. An exhaustive evaluation of the novel method is first performed on a scalar image sequence generated by direct numerical simulation of a turbulent 2-D flow. By qualitative comparisons, the method is then assessed on a METEOSAT image sequence.