In this paper the simulation results of Lake Baikal upper layers temperature regime are discussed. The Lake Baikal has a number of unique peculiarities, which distinguish it among others natural reservoirs. That is why the necessity of specializing model creating is appeared. This simulation was based on the experimental data that were obtained in period from March 2000 to February 2001 and from March 2004 to February 2005 in the framework of the Baikal Neutrino Telescope Project. The result of simulation is as follows: the effective diffusivity coefficient varies is enough to describe an averaging evolution of temperature profile. To simulate a fine structure of temperature profile as well as to simulate an anomalous variation of temperature, when a regular course of temperature is broken, the vertical mass-transfer coefficient is need. In the frame of chosen model possible scenarios of gomothermy and stable stratification formation are discussed.