Numerical simulations were carried out to determine the residence (or flushing) time of water in Vidy Bay (north shore of Lake Geneva) for different meteorological conditions. A hydrodynamic model (Delft3DFLOW) was applied to simulate the flow field in the embayment during 2010 and January 2011. Using these results, particle tracking was applied to estimate transport of wastewater effluent discharged into the embayment. The model predictions compared well with published field measurements of dissolved species (as given by electrical conductivity profiles) within the wastewater. The pelagic boundary of the embayment was defined by the largest within-bay gyre. Based on this definition, particle tracking was used to quantify the residence time under dominant wind conditions. Similarly, particle tracking was used to determine the travel time (i.e., time to exit the embayment) for each of Vidy Bay’s three inflows (stream, stormwater and wastewater effluent). Although the wind field over the lake is variable, current patterns in the embayment can be simulated using the hydrodynamic model forced by a spatially uniform wind field. For a given wind speed, the main factor influencing residence and travel times is the wind angle. The presence of gyres leads to high mean residence times with large variability. As the wind direction becomes more aligned with the shoreline (i.e., with increasing westerly or easterly components), longshore currents dominate. These disrupt gyre formation and markedly reduce the mean and variability of embayment residence time. The numerical model was utilized to assess the potential for plume movement (in plan) from above the wastewater effluent outfall towards one of Lausanne’s drinking water intakes. In the most direct pathway, westward longshore currents can move water from the embayment to the water column above the intake location.