River bars often form at river confluences due to variation in flow discharges or in sediment transport capacity; once these bars are grown, they constitute favourable habitats for vegetation development. In this work, we analysed the effect of vegetation above confluence bars on the hydrodynamics of a river reach. The case study considered is the Arno River reach at the Greve junction, where confluence bars expanded towards the opposite bank. A two-dimensional hydraulic model was implemented through BASEMENT software varying the flow discharge. Three-dimensional topographic data were used to generate the calculation mesh. Dendrometric surveys were carried out to describe the current state of the vegetation. Seven different vegetative scenarios were considered for numerical simulations, depending on different vegetation management conditions. Such scenarios are characterised by various plant densities, diameters, heights and species (herbaceous, shrub and arboreal), and, accordingly, different formulations were used to estimate the Manning coefficients. The outcomes of this study illustrate that the denser vegetation settled on confluence bars, the more the backwater effect is emphasised and the more the flow is shifted toward the opposite banks of the confluence thus inducing possible erosion phenomena at the toe of the outer bank. Moreover, the observed large bar extensions are surprising, when considering the mild confluence angle and the very low discharge ratio. We showed that the vegetation may be the key driver of the junction hydrodynamics and that vegetated confluences might not follow the classic hydraulics-related models which may describe only a formative configuration.