[Truncated abstract] The lake boundaries are an important source of sediment, nutrients and chemicals. For life inside the lake, the exchange between the lake boundaries (littoral) and lake interior (pelagic) is of central importance to Limnology as the net flux of nutrients into the water column is both the driving force and limiting factor for most algae blooms found during the stratification period. Consequently, the understanding of the relevant processes defining such an exchange is a further step toward a sound basis for future decisions by lake managers in order to ensure high water quality. The objective of this research was to investigate the physical processes responsible for the exchange of water and particles between the lake boundaries and the lake interior. An integrated approach using field experiments and 3D modelling as applied to Lake Kinneret (Israel) is presented. The field data revealed large-scale metalimnion oscillations with amplitudes up to 10 m in response to westerly diurnal winds, the existence of a well-defined suspended particle intrusion into the metalimnion of the lake, characterized by high concentrations of organic matter, and a well-mixed benthic boundary layer (BBL). The changes in the thermal structure explained the observed vertical and horizontal movements of the suspended particle intrusion. The horizontal advective transport via the metalimnion, associated with the velocities induced by the basin-scale mode-two Poincare wave, controlled the exchange between the lake boundaries and lake interior on daily time scales. The observed BBL over the lake slope varied markedly with time and space. Detailed comparison of simulation results with field data revealed that the model captured the lake hydrodynamics for time scales from hours to days. The model could then be used to extract the residual motions in the various regions of the lake. The residual motions below the surface layer were predominantly forced by the basin-scale internal wave motions, but the residual motion in the surface layer was found to be very sensitive to the curl of the wind field. The residual circulation was responsible for redistributing mass throughout the lake basin on time scales from days to weeks. A clear connection of dynamics of the BBL with the large-scale features of the flow was addressed. The time history of the mixing in the BBL and the resulting cross-shore flux was shown to vary with the phase of the basin-scale internal waves.