Lake Geneva, the largest freshwater lake in Western Europe, is subject to important environmental pressures from its densely populated shores and watershed. To maintain and improve water quality in this lake, as well as in other enclosed or semi‐enclosed basins, it is essential to understand and be able to predict how nutrients and pollutants are transported within it. A 3D numerical modeling study of Lagrangian transport in Lake Geneva is presented, showing the dispersion of water (based on tracking inert water particles) inflowing from the lake's main tributary, the Rhône River. The relation between dominant winds, circulation patterns, and transport was analyzed. The results demonstrated that transport within the lake is highly inhomogeneous in space and intermittent in time, because water mass movements are controlled by the wind‐induced formation of large‐scale gyres and their subsequent breakdown into smaller ones. Particle spreading was shown to be sensitive to the depth of the initial particle release, and to the mean depth of the particles’ trajectory. However, several preferential pathways could be identified. Some water particles rapidly (days) traveled across the entire lake, through the near‐shore region in the upper layer, while others remained trapped for months, particularly in the central region of the lake at depth. Deeper particles tended to remain longer in the lake, due to the insulating effect of stratification, bathymetry obstacles, and slower currents at greater depth.