The spatial variability of hydraulic conductivity is known to have a strong impact on solute spreading and mixing. In most investigations, its local anisotropy has been neglected. Recent studies have shown that spatially varying orientation in sedimentary anisotropy can lead to twisting flow enhancing transverse mixing, but most of these studies used geologically implausible geometries. We use an object‐based approach to generate stacked scour‐pool structures with either isotropic or anisotropic filling which are typically reported in glacial outwash deposits. We analyze how spatially variable isotropic conductivity and variation of internal anisotropy in these features impacts transverse plume deformation and both longitudinal and transverse spreading and mixing. In five test cases, either the scalar values of conductivity or the spatial orientation of its anisotropy is varied between the scour‐pool structures. Based on 100 random configurations, we compare the variability of velocity components, stretching and folding metrics, advective travel‐time distributions, one and two‐particle statistics in advective‐dispersive transport, and the flux‐related dilution indices for steady state advective‐dispersive transport among the five test cases. Variation in the orientation of internal anisotropy causes strong variability in the lateral velocity components, which leads to deformation in transverse directions and enhances transverse mixing, whereas it hardly affects the variability of the longitudinal velocity component and thus longitudinal spreading and mixing. The latter is controlled by the spatial variability in the scalar values of hydraulic conductivity. Our results demonstrate that sedimentary anisotropy is important for transverse mixing, whereas it may be neglected when considering longitudinal spreading and mixing.