Although it is primarily constituted in general from a limited variety of local plants, peat is however sensitive to physicochemical changes in the medium, in particular those induced by hydrological fluctuations. The present study aims at confronting the information on peat quality provided by various families of biochemical components (lipids, lignin, sugars), especially in order to check the validity of a new organic matter (OM) quality indicator, the “R400” index, directly drawn from Rock-Eval pyrolysis. This parameter, which is deduced from the sole S2 pyrolysis peak, is extremely robust. The Chautagne marsh, located between the Le Bourget Lake and the Rhône River lies in a key situation for recording lake level variations and Rhône River floods all along its Holocene filling. The study was conducted on a 6 m long core which comprises 4 m of peat under 66 cm of pedogenetically altered OM-rich sediment. Classical Rock-Eval pyrolysis revealed few qualitative and quantitative OM changes with Total Organic Carbon (TOC) values close to 50% and Hydrogen Index values around 300–350 mg HC g-1TOC in the peat. The R400 parameter remains practically unchanged in the upper unit affected by pedogenesis. It fluctuates however all along the peaty unit together with a progressive downward decrease, ascribable to diagenesis. Molecular analyses show that samples with high R400 values are richer in sugars and in slightly oxidized lignin. These results support the idea that the R400 parameter can be used as an indicator of OM preservation. Since OM preservation is mostly controlled by the water table in peat, the Chautagne marsh records hydrological fluctuations such as those of the Le Bourget Lake water level, all along the Holocene.