Optical analysis (palynofacies) of the organic matter (OM), occurring in various compartments (soils, bedrock formations, lacustrine chalks) of the lacustrine basin of Chaillexon (Doubs, France) has led to the definition of organic markers. Their variable contributions were observed in suspended matters taken over a period of a year (annual scale) and in lacustrine sediments covering the last 12,000 years B.P. (millennial scale). Results obtained lead to three main conclusions. Firstly, there exists a seasonal variation in the detrital organic fluxes, directly linked to the autumnal litter production. This allows us to distinct the detrital OM loaded during autumn-winter organic floods and spring-summer ones. Secondly, the organic record in Boreal to modern sediments of the lake of Chaillexon, fed by autumn-winter fluxes, appears mainly controlled by the autumnal productivity of vegetal biomass. Thirdly, the organic record does not point out a progressive evolution of organic fluxes linked with successive climatic phases. It shows abrupt ruptures of the balance (threshold effects) corresponding with the passage of the tree line in the watershed. These ruptures are not necessarily synchronous with climatic fluctuations.