The aim of this work is to analyse the formation mechanisms of large-scale coherent structures in the flow around a wall-mounted square cylinder, due to their impact on pollutant transport within cities. To this end, we assess causal relations between the modes of a reduced-order model obtained by applying proper orthogonal decomposition to high-fidelity simulation data of the flow case under study. The causal relations are identified using conditional transfer entropy, which is an information-theoretical quantity that estimates the amount of information contained in the past of one variable about another. This allows for an understanding of the origins and evolution of different phenomena in the flow, with the aim of identifying the modes responsible for the formation of the main vortical structures. Our approach unveils that vortex-breaker modes are the most causal modes, in particular, over higher-order modes, and no significant causal relationships were found for vortex-generator modes. We validate this technique by determining the causal relations present in the nine-equation model of near-wall turbulence developed by Moehlis et al. (New J. Phys., vol. 6, 2004, p. 56), which are in good agreement with literature results for turbulent channel flows.