This paper reports preliminary yet encouraging findings on the use of causal discovery methods to understand the interaction between atmospheric planetary- and synoptic-scale disturbances in the Northern Hemisphere. Specifically, constraint-based structure learning of probabilistic graphical models is applied to the spherical harmonics decomposition of the daily 500-hPa geopotential height field in boreal winter for the period 1948–2015. Active causal pathways among different spherical harmonics components are identified and documented in the form of a temporal probabilistic graphical model. Since, by definition, the structure learning algorithm used here only robustly identifies linear causal effects, we report only causal pathways between two groups of disturbances with sufficiently large differences in temporal and/or spatial scales, that is, planetary-scale (mainly zonal wavenumbers 1–3) and synoptic-scale disturbances (mainly zonal wavenumbers 6–8). Daily reconstruction of geopotential heights using only interacting scales suggest that the modulation of synoptic-scale disturbances by planetary-scale disturbances is best characterized by the flow of information from a zonal wavenumber-1 disturbance to a synoptic-scale circumglobal wave train whose amplitude peaks at the North Pacific and North Atlantic storm-track region. The feedback of synoptic-scale to planetary-scale disturbances manifests itself as a zonal wavenumber-2 structure driven by synoptic-eddy momentum fluxes. This wavenumber-2 structure locally enhances the East Asian trough and western Europe ridge of the wavenumber-1 planetary-scale disturbance that actively modulates the activity of synoptic-scale disturbances. The winter-mean amplitude of the actively interacting disturbances are characterized by pronounced fluctuations across interannual to decadal time scales.