Climate change models predict a possible increase in air temperature of 2–8°C. This means that global warming will significantly affect the functioning of various types of hydrogenic ecosystems. However, the effect of the temperature increase on microbial loop function in small water bodies associated with peat ecosystems (peat pools and Sphagnum hollows) is still unknown. We used mesocosm experiments (control and treatments with a 2°C, 4°C and 8°C temperature increase) to determine the response of bacterioplankton, flagellates, testate amoebae and ciliates to simulated temperature changes, taking into account seasonal variation in the temperate climate zone. The simulated increase in climate warming increased the species richness of ciliates and the abundance of bacteria, flagellates and ciliates. In contrast, there was a decrease in the species number and abundance of testate amoebae, the top predators in peat ecosystems. The sensitivity of the various microbial groups to temperature was size-dependent; large-sized testate amoebae declined under warming. These shifts caused a decrease in the predator–prey mass ratio. An increase in the abundance of top predators promotes increased abundance of ciliates, and thus changes the architecture of the food web. At the same time, we observed the increase in phycoflora biomass thus can cancel the potential negative effects of warming on heterotrophic microbial activity. So, the potential effect of warming on the C budgets of peat pools and hollows is evident. A better understanding of what regulates microbial populations and activity in small reservoirs in peat bogs and unravelling of these fundamental mechanisms are particularly critical to more accurately predict how peat bogs will respond to climate disturbances.