Abstract A palaeolimnological study, covering the last c. 12,000 years, was conducted in a small subalpine lake located in the Alps to study climate change impacts on carbon flows through food webs in small lakes. We used analysis of sedimentary pigments and carbon stable isotopic composition of chironomid remains (δ13CHC) to reconstruct past dynamics of phytoplankton community and carbon sources sustaining benthic consumers. Chironomid biomass was sustained by a combination of allochthonous, autochthonous and CH4‐derived organic matters, and their relative contributions were correlated to changes in temperature. Relatively high terrestrial contributions to chironomid biomass were observed during period of the Holocene when in‐lake production was low. Relatively high incorporation of CH4‐derived carbon to chironomid biomass was found during anoxic events co‐occurring with the Holocene thermal maximum. Results were then compared with those collected in a small boreal lake in Estonia. We tested the hypothesis that responses in carbon flows through benthic food web to past climate change would be similar between these lakes. We found a negative correlation between δ13CHC values of both lakes and inferred air temperature, suggesting that temperature was the major driver to different food sources being incorporated into chironomid biomass. Our study demonstrated that air temperature was the principal driver of the energy flows through benthic food web in the studied small lakes. We conjectured that carbon cycling in food webs of small lakes might be strongly sensitive to climate change.