Arrays of real mangrove pneumatophores (i.e. aboveground pencil roots) and artificial dowel mimics were constructed in a laboratory flume to examine differences in canopy flow dynamics. Compared to the uniform-height dowel canopy, the non-uniform height of the pneumatophores significantly reduced the intensity of the canopy shear, and shifted the turbulence maxima observed directly above the dowels upwards by approximately the standard deviation of the pneumatophore heights. Consequently, bed shear stresses were up to two times greater in the uniform-height dowel canopy than in a pneumatophore canopy of similar density. At the same time, ratios of the within-canopy velocity to the free-stream velocity above the canopies were not significantly altered by the heterogeneous height, shape and spatial distribution of the pneumatophores. Our results emphasize that uniform dowels are poor proxies of real pneumatophore canopies and may lead to underestimations of sediment-trapping efficiency.