I tested the hypothesis that the quantity and quality of suspended and sediment organic matter in shallow coastal waters is affected by wind-induced resuspension at a smaller depth scale (< 1 m) than usually assumed. Water and sediment surface (0 to 1 cm) samples were collected on a seasonal basis and analyzed for total suspended matter, organic fraction, and phytopigments at 12 shallow sites representing a depth gradient from 0.2 to 2.0 m along the western shore of Sicily. Water column concentrations of all measured variables decreased rapidly with increasing water column depth, and concentrations levelled off at about 1 m water column depth. The likelihood of sediment resuspension by wind for various combinations of water column depth and fetch length was modelled using the CERC (U.S. Army Corps of Engineers, Coastal Engineering Centre, Washington D.C. US) model for 10 years of local wind data. The simulations indicated that even light winds (2 m s⁻¹) increased the likelihood of resuspension in the shallowest basin (0.2 m depth) with an effective fetch of 250 m. This study provides evidence that shallow water systems should not be investigated by considering the entire water column as a single homogenous layer. Investigations of shallow water ecosystems should consider 2 main layers with different ecological conditions and functions: a shallow surface turbulent layer from the surface to a depth of 1 m that is strongly affected by wind-driven physical forces and a deeper, below 1 m to the sediment surface, layer where wind-driven turbulence has less impact.