An in-house fully three-dimensional general-purpose finite element model is applied to solve the hydrodynamic structure in a periodic Kinoshita-generated meandering channel. The numerical model solves the incompressible Reynolds-averaged Navier–Stokes equations for mass and momentum, while solving the k − ε equations for turbulence. The free surface is described by the rigid-lid approximation (using measured water surface data) for flat (smooth-bed) and self-formed (rough-bed) conditions. The model results are compared against experimental measurements in the ‘Kinoshita channel’, where three-dimensional flow velocities and turbulence parameters were measured. This validation was carried out for the upstream-valley meander bend orientation under smooth (flat bed) conditions. After validation, several simulations were carried out to predict the hydrodynamics in conditions where either it was not possible to perform measurements (e.g. applicability of the laboratory acoustic instruments) and to extrapolate the model to other planform configurations. For the flat smooth-bed case, a symmetric (no skewness) planform configuration was modeled and compared to the upstream-skewed case. For the self-formed rough-bed case, prediction of the hydrodynamics during the progression of bedforms was performed. It appears that the presence of bedforms on a bend has the following effects: (i) the natural secondary flow of the bend is disrupted by the presence of the bedforms, thus depending on the location of the dune, secondary flows might differ completely from the traditional orientation; (ii) an increment on both the bed and bank shear stresses is induced, having as much as 50% more fluvial erosion, and thus a potential increment on the migration rate of the bend. Implications on sediment transport and bend morphodynamics are also discussed in the paper. Copyright © 2013 John Wiley & Sons, Ltd.