Flow disturbances generated by individual patches of submerged, flexible aquatic vegetation were investigated for two naturally growing macrophyte species, Potamogeton crispus L. and Myriophyllum spicatum L., in a sandy lowland river. Through acoustic Doppler velocimetry, 24 vertical profiles of the 3D velocity field were recorded downstream of each of the patches. The morphological features and biomechanical properties of the plants were also evaluated. The experiments showed the relationship between biomechanical characteristics and turbulence statistics. M. spicatum, which was stiffer and therefore less prone to dynamic reconfiguration, showed a greater effect on velocity damping, causing an increase in Reynold stresses, turbulence intensities, and turbulent kinetic energy downstream of the patch. These effects were present in regions both above and below plant height. In contrast for P. crispus, these effects were present only below plant height. The stiffer plant produced a mixing layer in its wake similar to that of dense plant canopies. The patch of less stiff and more streamlined P. crispus with longer leaves presented a much weaker effect on the flow. In contrast to previous studies conducted with rigid plant surrogates, we concluded that reconfiguration of the living flexible plants allows the plants to minimize drag forces, and therefore, their influence on the flow field was weaker than the effects reported for rigid surrogates.