We experimentally manipulated the thermal environment in laboratory mesocosms to evaluate the effect of temperature on organic matter transformation in two systems of lower and higher ambient nutrient availability. We used a system of 6 mesocosms, equipped with heating and cooling systems; 3 were filled with water from a mesotrophic lake and 3 with water from a eutrophic lake. Each of the 3 mesocosms were maintained at different temperatures: ambient lake temperature (10 °C and 20 °C), ambient +5 °C, and ambient +10 °C and the experiment was replicated in twice, in the spring and summer seasons. We measured rates of physicochemical and bacteriological parameters changes over a 2-day period. Results of the study demonstrated that, irrespective of nutrient concentration, an increase in temperature resulted in enhanced the level of labile organic matter, indicated by significantly elevated concentrations of dissolved organic carbon (DOC) and low values of SUVA (specific UV absorbance. = Abs 260·1000/DOC). The effect of temperature was stronger in the lower nutrient concentration in the spring experiment treatments elevated by 5 °C. The increase in temperature was additionally accompanied by significant increased total bacterial counts (TBC), biomass (BB) and heterogeneity of bacterioplankton. In the higher nutrient concentration, the increase in temperature exerted a greater influence on the dynamics of concentration of heteromorphic organic matter, shown by the negative correlation between particulate organic carbon (POC) and DOC content and TBC value. The accumulation of considerable quantities of refractory DOC and POC and low bacterioplankton activity may intensify the rate of degradation of eutrophic lake ecosystems.