Understanding flow structures in urban areas is widely recognized as a challenging concern due to its effect on urban development, air quality, and pollutant dispersion. In this study, state-of-the-art data-driven methods for modal analysis of simplified urban flows are used to study the dominant flow processes in these environments. Higher order dynamic mode decomposition (HODMD), a highly-efficient method to analyze turbulent flows, is used together with traditional techniques such as proper-orthogonal decomposition (POD) to analyze high-fidelity simulation data of a simplified urban environment. Furthermore, the spatio-temporal Koopman decomposition (STKD) will be applied to the temporal modes obtained with HODMD to perform spatial analysis. The flow interaction within the canopy influences the flow structures, particularly the arch vortex. The latter is a vortical structure generally found downstream of wall-mounted obstacles, which is generated as a consequence of flow separation. Therefore, the main objective of the present study is to characterize the mechanisms that promote these phenomena in urban areas with different geometries. Remarkably, among all the vortical structures identified by the HODMD algorithm, low- and high-frequency modes are classified according to their relation with the arch vortex. They are referred to as vortex-generator and vortex-breaker modes, respectively. This classification implies that one of the processes driving the formation and destruction of major vortical structures in between the buildings is the interaction between low- and high-frequency structures. The high energy revealed by the POD for the vortex-breaker modes points to this destruction process as the mechanism driving the flow dynamics. Furthermore, the results obtained with the STKD method show how the generating- and breaking-mechanisms originated along with the streamwise and spanwise directions.