The in situ effect of biological activity on herbicide degradation was studied in sediment. Early diagenesis indicators of organic matter (OM) was selected to provide information on the presence and the kinetics of the various biotic and abiotic processes involved in the degradation of fresh organic matter, the vector of herbicides in sediment. Two tandem-coring samples were taken in the Malause reservoir, one in the hyperoxic zone (Tarn confluence, MT core) and the other in the central part, under the exclusive influence of the Garonne River (MG core), after having crossed a zone where the high intensity of abiotic processes is proven. At each site, analysis of the vertical profile of the herbicides was coupled with compounds associated with early diagenesis of OM. The MT core proved nearly seven times more contaminated than the MG core. DEA played a minor role in sediment contamination. Biological activity only seems to influence herbicide degradation indirectly. Neither oxygen concentration nor the level of labile carbon indicated any correlation between the consumption of fresh organic matter and substrate degradation. Herbicide transformation thus does not seem to depend on the consortia studied but on physicochemical parameters such as hydrolysis, leading to the long half-life of herbicides in sediment and hence their long-term presence in the aquatic environment.