The dynamics of turbulent flow structures in the wakes of barchan dunes is investigated to understand the complex, long-range interactions that occur between these three-dimensional bedforms. High-frame-rate stereo-particle image velocimetry measurements are collected from the cross-stream plane in a refractive-index-matched flume, wherein rigid models are immersed in the logarithmic region of a turbulent boundary layer. Through application of Taylor's hypothesis, limited-domain pseudo-three-dimensional reconstructions of the flow are made, wherein coherent structures are identified in the wake of an isolated barchan that resemble hairpin-like vortices. Amplitude modulation analysis, based on wavelet decomposition of velocity fluctuations and swirling strength, suggests a correlation between the shedding of these coherent structures and the passage of large-scale motions (LSMs) aloft in the turbulent boundary layer within which the barchan dune is immersed. Impulse analysis of shear stress events shows that, while the hairpin-like structures predominantly induce ejections of low-momentum fluid, the intermittent passage of an overlying high-momentum LSM yields intense sweep events as they impact the wall. Similar flow dynamics is found in dune–dune collision configurations involving barchan dunes arranged in tandem, with the exception that significant flow asymmetries are introduced, resulting in structures resembling single-legged hairpin-like (or ‘cane’) vortices being identified in conditional averages. These results provide insight into both the morphodynamics of dune interactions as well as the interactions between boundary-layer structure and roughness elements protruding into the log layer.