The nonlinear hydrodynamics (3D RANS model) in a wide semi-enclosed windy lagoonal ecosystem is accurately investigated in the context of analyzing the limiting conditions of the recovery of submerged aquatic vegetation (SAV). Among the main natural hydrodynamical forcings, we consider the wind effect. We mainly focus attention to characteristic velocities (free surface and bottom) and to free surface elevation in the nearshore regions (with shallow water) where SAV were severely damaged in the past decades. Our main result relates to wind effects that form downwind coastal jets, alongshore, in shallow water areas, due to Berre bathymetry. Such coastal jets, which were never described previously in Berre lagoon literature, give rise to substantial bottom currents in the shallower areas which could be responsible of changing the composition of mud-sand sediments; such changes are recognized in the literature to be a limiting factor for SAV recovery. (c) 2013 Elsevier Ltd. All rights reserved.