Recent results from a tracer release experiment have shown that, similar to many lakes and ocean basins, deep-water mixing in the Baltic Sea is largely determined by mixing processes occurring in the energetic near-bottom region. Due to the complexity and small vertical extent of this region, however, previous modeling studies of the Baltic Sea have so far not been able to provide a numerically and physically sound representation of boundary mixing. Here we discuss first results from a nested high-resolution simulation of the central Baltic Sea that aims at a realistic description of the turbulent bottom boundary layer with the help of new numerical techniques (adaptive coordinates) and state-of-the-art turbulence modeling. Using a comprehensive data set from the Baltic Sea Tracer Release Experiment, we show that the model is able to reproduce the key dynamical processes (near-inertial waves, topographic waves, and a rim current) with excellent accuracy. Boundary mixing triggered by these processes was found to result in simulated basin-scale mixing rates in close agreement with observations, including a seasonal variability that has been emphasized in previous studies. These results may be relevant also for the description of mixing in large lakes and other stratified basins.