The overarching aim of this paper is to investigate the lake ecosystem response to different drivers over a long term period by a paleolimnological study in Lake Narlay (46°64N, 5°91E) located in the Jura Mountains of France. It is a small, hard-water lake with a maximum water depth of 40 m and extended anoxic condition of the bottom water. Previous results on sediments analysis have documented a differential response of the lake to the environmental changes that occurred in AD 1600 when major shift in the trophic reliance on methane of the benthic food web were observed. From 1920 with intensification of modern agriculture, animal farming and the construction of a cheese making facility, the lake become eutrophic, with Oscillatoria rubescens bloom. However, the lake showed pronounced changes in an older period that remained unanswered. In this paper we aim at reconstructing in more detail the limnological conditions of this Lake over the last 1200 yrs. using combined analyses of specific algal carotenoids and subfossil diatom remains. A comparison with other proxies (chironomid, pollen, and instrumental climatic reconstruction) will be used to better identify, between the complex combination of climate and anthropogenic pressure, the driving factors that determined the ecological trajectory of Lake Narlay.