Lakes are valuable natural resources. However, they are increasingly threatened by anthropogenic activities. Transport and mixing processes, which govern the distribution of chemical and biological constituents, play a crucial role in sustaining lake ecology. Understanding these complex processes can help us protect these precious resources and use them wisely. In order to better quantify the flux pathway of constituents in Lake Alpnach, in this study, mixing processes in Lake Alpnach were simulated by a two-dimensional model (CE-QUAL-W2). The model exhibited very strong capabilities in simulating large time scale events such as the second vertical seiche mode, temperature and velocity changes; this set a consistent starting point for further water-quality-oriented simulations. Nevertheless the model displayed weaknesses in predicting velocity fluctuations and small time-scale waves (< about 7 hours), which may be source of errors in other lakes or in short time simulations. Vertical diffusivity (Heat-Budget Method) was also calculated in this study, in order to better characterize mixing. It was proven that reliable vertical diffusivity can be calculated from CTD data alone, although the coupling CTD-Thermistor chains will provide more accurate results.