Most of the existing works on vegetated flows are based on experimental tests in smooth channel beds with staggered-arranged rigid/flexible vegetation stems. Actually, a riverbed is characterized by other roughness elements, i.e., sediments, which have important implications on the development of the turbulence structures, especially in the near-bed flow zone. Thus, the aim of this experimental study was to explore for the first time the turbulence anisotropy of flows through emergent rigid vegetation on rough beds, using the so-called anisotropy invariant maps (AIMs). Toward this end, an experimental investigation, based on Acoustic Doppler Velocimeter (ADV) measures, was performed in a laboratory flume and consisted of three runs with different bed sediment size. In order to comprehend the mean flow conditions, the present study firstly analyzed and discussed the time-averaged velocity, the Reynolds shear stresses, the viscous stresses, and the vorticity fields in the free stream region. The analysis of the AIMs showed that the combined effect of vegetation and bed roughness causes the evolution of the turbulence from the quasi-three-dimensional isotropy to axisymmetric anisotropy approaching the bed surface. This confirms that, as the effects of the bed roughness diminish, the turbulence tends to an isotropic state. This behavior is more evident for the run with the lowest bed sediment diameter. Furthermore, it was revealed that also the topographical configuration of the bed surface has a strong impact on the turbulent characteristics of the flow.