The influence of surface heterogeneities extends vertically within the atmospheric surface layer to the so-called blending height, causing changes in the fluxes of momentum and scalars. Inside this region the turbulence structure cannot be treated as horizontally homogeneous; it is highly dependent on the local surface roughness, the buoyancy and the horizontal scale of heterogeneity. The present study analyzes the change in scalar flux induced by the presence of a large wind farm installed across a heterogeneously rough surface. The change in the internal atmospheric boundary-layer structure due to the large wind farm is decomposed and the change in the overall surface scalar flux is assessed. The equilibrium length scale characteristic of surface roughness transitions is found to be determined by the relative position of the smooth-to-rough transition and the wind turbines. It is shown that the change induced by large wind farms on the scalar flux is of the same order of magnitude as the adjustment they naturally undergo due to surface patchiness.