In this study, we investigate the changes in flow structure at the interface of a partly vegetated section and determine whether it is better to have wholly vegetated test sections near important riverine structures. We analyze the flow behaviour at the interface using the transverse flux, turbulent kinetic energy, probability density function, and anisotropy. We observed a helical flow downstream of the partly vegetated section, indicated by a negative Reynolds shear stress. The lateral acceleration of the flow contributes to large-scale fluctuations, confirmed by a probability density function analysis and anisotropy stress tensor. The turbulent kinetic energy was higher for the wholly vegetated case due to the presence of two-dimensional stress components compared to one-dimensional stress components in the partly vegetated case, confirmed by an anisotropy invariant map. Wholly vegetated sections exhibited a highly fluctuating transverse flux, indicating a larger intermixing rather than a unidirectional movement. Based on the findings, it is recommended to opt for a wholly vegetated cover instead of a partly vegetated cover in riverbanks or near structures such as bridge piers and river training structures affected by a lateral or laterally accelerating flow. The analysis of an additional turbulence helps safer designs of critical components of river structures.