A three-dimensional large-eddy simulation (LES) model, which includes the effects of plant–atmosphere interactions, is used to study the effects of surface inhomogeneities on near-surface coherent structures over an open field and behind a forest canopy. These simulated conditions are representative of two wind sectors of the Site Instrumental de Recherche par Teledetection Atmospherique (SIRTA) experimental site at the Institut Pierre Simon Laplace, Palaiseau, France. Coherent structure properties deduced from wavelet transforms of the simulated near-surface vertical velocity time series are not modified by upstream terrain heterogeneities, in agreement with site measurements. This feature is related to the nature of structures detected from the vertical velocity time series. The turbulence close to the surface seems composed of both local coherent structures and large coherent structures reflecting outer-layer properties, which depend on the overall surface heterogeneity or upstream heterogeneity. It is argued that the streamwise velocity is representative of these large outer-layer structures that impinge onto the ground through a top-down mechanism as identified through the space–time correlation of the wind velocity components. In contrast, the vertical velocity is more representative of small structures resulting from the impingement of the large outer-layer structures. These small structures represent locally-generated, active turbulence, which adjusts rapidly to local surface conditions, and consequently they are only weakly dependent on upstream heterogeneities.