This study aims at reconstructing the limnological conditions of Lake Narlay, a lake of which a previous study has shown major changes in the trophic reliance on methane of the benthic food web. The evolution of environmental and limnological conditions in and around Lake Narlay is reconstructed using combined analyses of subfossil chironomid remains, sedimentary pigments and organic carbon accumulation rates; whereas potential driving factors are reconstructed by pollen and coprophilous analyses and the use of climate paleo-records. The results suggest a complex combination of climate and anthropogenic pressure to explain the 1200 years of ecological trajectory of Lake Narlay. This ecological trajectory seems to be firstly control by climatic variability, because the colder event of the Little Ice Age induces a significant impact on chironomid assemblage, organic matter influx, and lake productivity. In a more recent time, the anthropogenic control seems to become predominant. The intensification of the agro-pastoral practices in the catchment area of Lake Narlay seems to induce the degradation of the oxygen conditions at the water/sediment interface. In addition, the present study gives also lines of evidence that the human intensification in the watershed of Lake Narlay seems to be the main cause of the major change in the contribution of biogenic methane to the benthic food web. However, the transition stage between the two trophic pathways (from absence to transfer of biogenic methane) involves a progressive change with intermediate limnological conditions, making the assessment of a tipping point in the temporal evolution difficult. Better knowledge of the relationships between the temporal evolution of limnological conditions and the activation of the trophic reliance on methane will require the study of other sites with different conditions.