Learning the dependency structure between spatially distributed observations of a spatio-temporal process is an important problem in many fields such as geology, geophysics, atmospheric sciences, oceanography, etc. . However, estimation of such systems is complicated by the fact that they exhibit dynamics at multiple scales of space and time arising due to a combination of diffusion and convection/advection. As we show, time-series graphical models based on vector auto-regressive processes are inefficient in capturing such multi-scale structure. In this paper, we present a hierarchical graphical model with physically derived priors that better represents the multi-scale character of these dynamical systems. We also propose algorithms to efficiently estimate the interaction structure from data. We demonstrate results on a general class of problems arising in exploration geophysics by discovering graphical structure that is physically meaningful and provide evidence of its advantages over alternative approaches.