River morphological change is the complex evolution of riverbed states, which can lead to serious riverbank failures, and is a worldwide concern. However, revealing the cause of the evolution, in particular, the potential morphological scouring by eddy currents, is difficult. Accordingly, we propose a comprehensive combination of 2D and 3D simulations to reveal the eddy currents. We selected the Vam Nao, part of the Mekong River, with semi-tidal effects and confluence flows as the case study. We created two unstructured 40 m × 40 m triangular meshes using inverse distance interpolation. This study used the Saint–Venant equations (TELEMAC2D) and Navier–Stokes equations (TELEMAC3D) to reveal the eddy currents for 2009, 2017, and 2018. TELEMAC2D (the simplified form of TELEMAC3D) was assessed for 15 days, 3 months, and 1 year, which met a satisfactory level. The eddy currents’ appearance was verified by local knowledge. We found recirculating currents near the riverbank to the East (right at the riverbank failures), whose velocity was approximately half and 1/3–1/4 of the mainstream flow velocity in the dry and flood seasons, respectively. Our study approach performed well in revealing the eddy currents, which can aid in assessing potential riverbank failures and can be applicable to similar contexts.