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The present study investigates flow dynamics in the hub region of a wind turbine focusing on the influence of nacelle geometry on the root aerodynamics by means of Reynolds averaged Navier–Stokes simulations with the code FLOWer. The turbine considered is a generic version of the Enercon E44 converter incorporating blades with flat-back-profiled root sections. First, a comparison is drawn between an isolated rotor assumption and a setup including the baseline nacelle geometry in order to elaborate the basic flow features of the blade root. It was found that the nacelle reduces the trailed circulation of the root vortices and improves aerodynamic efficiency for the inner portion of the rotor; on the other hand, it induces a complex vortex system at the juncture to the blade that causes flow separation. The origin of these effects is analyzed in detail. In a second step, the effects of basic geometric parameters describing the nacelle have been analyzed with the purpose of increasing the aerodynamic efficiency in the root region. Therefore, three modification categories have been addressed: the first alters the nacelle diameter, the second varies the blade position relative to the nacelle and the third comprises modifications in the vicinity of the blade–nacelle junction. The impact of the geometrical modifications on the local flow physics are discussed and assessed with respect to aerodynamic performance in the blade root region. It was found that increasing the nacelle diameter deteriorates the root aerodynamics, since the flow separation becomes more pronounced. Possible solutions identified to reduce the flow separation are a shift of the blade in the direction of the rotation or the installation of a fairing fillet in the junction between the blade and the nacelle.