A computational fluid dynamics model is presented for the calculation of the flow, suspended solids, and tracer concentration fields in the settling tanks of the water treatment plant of Aharnes, an important component of the water supply system of the greater area of Athens, Greece. The model is applied to investigate the expected negative effect of the wind on the hydraulic and settling performance of the tanks and to evaluate the improvement resulting from the installation of one and two baffles; the wind is modeled using a simple and very conservative approach that involves the setting of a constant horizontal flow velocity on the free surface. The model is calibrated and verified with field turbidity measurements. Calculations show that the effect of wind on the flow field and the hydraulic efficiency is strong, with the creation of massive re-circulation areas with intense mixing and high short circuiting; however, the effect of wind on the settling performance of the tanks is not pronounced. The removal efficiency of the tanks, which is 72.48% in calm conditions, is reduced to 68.07% for windy conditions; moreover, it increases to 70.00 and 71.04%, when one or two baffles are installed, respectively.