We conducted a whole-lake experiment by manipulating the stratification pattern (thermocline depth) of a small polyhumic, boreal lake (Halsjärvi) in southern Finland and studying the impacts on lake mercury chemistry. The experimental lake was compared to a nearby reference site (Valkea-Kotinen Lake). During the first phase of the experiment the thermocline of Halsjärvi was lowered in order to simulate the estimated increase in wind speed and in total lake heat content (high-change climate scenario). The rate of methyl mercury (MeHg) production during summer stagnation (May-August) was calculated from water profiles before the treatment (2004), during treatment (2005, 2006) and after treatment (2007). We also calculated fluxes of MeHg from the epilimnion and from the hypolimnion to the sediments using sediment traps. Experimental mixing with a submerged propeller caused a 1.5-2 m deepening of the thermocline and oxycline. Methyl mercury production occurred mostly in the oxygen free layers in both lakes. In the experimental lake there was no net increase in MeHg during the experiment and following year; whereas the reference lake showed net production for all years. We conclude that the new exposed epilimnetic sediments caused by a lowering of the thermocline were a major sink for MeHg in the epilimnion. The results demonstrate that in-lake MeHg production can be manipulated in small lakes with anoxic hypolimnia during summer. The climate change induced changes in small boreal lakes most probably affect methyl mercury production and depend on the lake characteristics and stratification pattern. The results support the hypothesis that possible oxygen related changes caused by climate change are more important than possible temperature changes in small polyhumic lakes with regularly occurring oxygen deficiency in the hypolimnion.