Sedimentation is a key process in lake functioning, and plays an important role in nutrient and carbon cycles at both regional and global scales. Several biological processes have been shown as quantitatively affecting sedimentation, but very few works have tried to relate the structure of aquatic communities and the quality of sinking organic matter. We tested in a mesocosm study how food-web structure affects quantitatively and qualitatively sedimentation in eutrophic systems. We carried out a long-term experiment (14 months) in large replicated enclosures either dominated by planktivorous fish or fishless. Food-web structure modified the specific composition of zooplankton communities and phytoplankton biomass, as expected by the trophic cascade theory. Planktivorous fish had a strong positive effect on gross sedimentation rate, but the fraction of suspended particulate material that sank only slightly differed between treatments. The density of transparent exopolymer particles (TEP) was a good descriptor of sedimentation rate, highlighting the key role of these polysaccharidic particles in sinking processes. In fish enclosures, sediment elemental ratios were positively related to seston elemental ratios, suggesting the dominance of algal sedimentation. In fishless mesocosms, N/P ratios of sinking material and of zooplankton showed a strong negative relationship, indicative of a major contribution of zooplankton-egested material to sinking particles. Analyses of free lipids in sediments confirmed the distinct origins of sinking material. Despite the absence of clear elemental composition distinctions between the two types of sediment, food-web structure strongly modified sediment biochemical composition.