Instrumental data about lake functioning before anthropogenic disturbances of the last century are scarce and often discontinuous. A paleolimnological study through sedimentological, geochemical (mineral and organic), chironomid and diatom assemblages analyses has been applied to reconstruct the trophic state and hypolimnion oxygenation changes in Lake Bourget during the last century. This approach presents also the interest to permit the access to the reference state of lake in the sense of the European Framework Directive. Lake sediments are characterized by the appearance of biochemical varves (confirmed by radionuclide dating) associated with a decreasing in oxygen concentration in the lake bottom. These biochemical varves are generally composed of three layers: a spring diatom lamina, a spring/summer bio-precipitated calcite-rich lamina and a winter lamina rich in organic matter and detrital particles. The eutrophication and the first anoxic facies appeared simultaneously in AD 1943 +/- 1 year. This eutrophication was indicated by drastic increase in biogenic silica (mostly diatoms), changes in diatom assemblages (with the development and dominance of taxa typical for eutrophic lakes), larger calcite crystals (15-30µm) and an increase in the accumulation of lacustrine organic matter. The rise in planktonic production in the upper zone of the water column overwhelmed the capacities of consumers to assimilate this organic matter which highly accumulated in the sediment leading to hypoxia (and anoxia) in the hypolimnion. The eutrophication is mostly caused by the inflow of untreated sewage effluents, and – to a lesser extent – by non-point phosphorous source coming from the lake catchment area. The preservation state of laminations and the presence of some oxybiontic chironomid taxa suggest the prevalence of less harsh hypoxia between 1943 and 1960 AD than since 1960 AD. In order to improve lake water quality, waste waters were treated and diverted directly to the Rhone in 1980. However, about 14 years were necessary to improve nutrient inputs in lake water surface. Indeed, from AD 1995 to 2006, the diatom assemblages suggest a reduction in nutrients, and a return to mesotrophic conditions, a result of improved wastewater management. Until 2006, no change in hypolimnion benthic conditions has been shown, neither from the organic matter content, the geochemical characteristics of the sediments or the subfossil chironomid profundal community.