Based on long-term observations carried out from onboard scientific research vessels, relationships have been established between transparency by Secchi disk and temperature of upper water layer in Southern Baikal. Peculiarities of the relationships in different hydrological seasons and factors caused these peculiarities have been discussed. In summer and autumn, negative correlation between parameters is due to the influence of temperature on phytoplankton growth. The reason of positive correlation in spring and early winter is the effect of water temperature on the intensity of vertical mixing. The relationships established allow revealing long-term trend in transparency by Secchi disk during the warming period in 1940-2000. Data on transparency measurements of 1950-1987 confirm the conclusion that transparency increases in spring months and decreases in summer and autumn.