In this paper, we face the challenging problem of estimation of time-consistent layer motion fields at various atmospheric depths. Based on a vertical decomposition of the atmosphere, we propose three different dense motion estimator relying on multi-layer dynamical models. In the first method, we propose a mass conservation model which constitutes the physical background of a multi-layer dense estimator. In the perspective of adapting motion analysis to atmospheric motion, we propose in this method a two-stage decomposition estimation scheme. The second method proposed in this paper relying on a 3D physical model for a stack of interacting layers allows us to recover a vertical motion information. In the last method, we use the exact shall...