Secondary flows induced by the blocking effect of a river plume on a transverse upwelling are investigated in a microtidal region of freshwater influence (ROFI). A nested version of the SYMPHONIE primitive-equation free-surface model for 3-D baroclinic coastal flows has been developed for the Rhône ROFI. The main characteristics of the model are a generalized sigma coordinate system in finite differences, using a time splitting for external and internal modes and high-order numerical advection schemes for density fields in combination with an modified turbulence closure scheme. The nesting system consists of two grids forced by the high-resolution ALADIN model atmospheric data. The coarse grid of 3 km resolution for the whole Gulf of Lions allows the forcing of the Liguro-Provençal large-scale current when the fine mesh of 1-km resolution is centred on the river mouth of the Grand Rhône. Documented field experiments from the Biodypar 3 field campaign performed during March 1999 are used for validation. Numerical results, CTD profiles and a SPOT TSM visible image are in good agreement concerning the shape and structure of the river plume. Other coastal flow features can be observed from satellite imagery. Computations of realistic situations recover these main secondary structures. Complementary process-oriented runs give an explanation of how the coastal upwelling induced by an inhomogeneous offshore wind is destabilized by the combination of the river plume and along-shelf current-blocking effects. In the end, a factor-separation analysis provides evidence that the locally non-linear effects in momentum contribute to the occurrence of secondary vortices.