This study deals with the role of bioturbation in the early diagenesis of freshwater sediments, particularly the effects of the diversity of the biological transports. To understand the complex interactions between the bio-transports and the reactions of matter transformation, some models of reactive transport were developed including the bio-transport diversity. In a first chapter, cadmium transport by oligochætes tubificids was modelled using an existing dataset. Then, the more complex case of the organic matter mineralization in the Malause reservoir (West South of France) has been addressed. Bioturbation by the natural benthic community was measured. A model of early diagenesis of organic matter was developed including this bioturbation, and particularly the non-local transports. Finally, an extension of bioturbation models is proposed in the last chapter, to account for the effects of the patchiness in the distribution of bioturbators.