Inter-basin exchange of water and dissolved substances in lakes is often limited by topographic constrictions leading to spatially heterogeneous distributions of nutrients and plankton. Here, we identify the main factors controlling inter-basin exchange on seasonal and inter-annual time scales and investigate the impact of changes in climate and hydrology focusing mainly on the exchange between two basins of Lower Lake Constance (LLC). The analysis is based on multi-annual simulations of LLC, a sensitivity analysis, and numerical tracer experiments with a coupled 3-D hydrodynamic ice model (AEM3D). The seasonal course of water exchange is predominantly determined by the seasonal change in the current speed across the sill, v_S, but also by changes in the area of the cross-section above the sill resulting from water level changes. The seasonal pattern of v_S is linked to the presence of ice cover, the seasonal change in stratification and in water level. The impact of climate warming and hydrological change on water exchange therefore varies seasonally. Climate warming results in reduced ice cover and an earlier onset and longer duration of stratification, leading to enhanced inter-basin exchange especially during winter and spring, but not in summer. In contrast, increased water levels enhance inter-basin exchange especially in summer, because the increase in cross-sectional area associated with increased water levels coincides then with high v_S. Finally, the fraction of water from Upper Lake Constance reaching the rather secluded basin Gnadensee increases with climate warming, implying a larger influence of the upstream conditions on Gnadensee.