Estuaries are important ecosystems from environmental and economical point of views and are the place of numerous transformations of organic matter (OM) during the transfer from land to the ocean. The dynamics of OM in estuarine systems is complex and was only rarely investigated at the structural or molecular level, even though OM transformation in the estuarine aquatic and sediment compartments involves processes taking place at this level. The aim of this study was to constrain the sources and fate of the OM in the Seine Estuary, one of the largest estuaries in France. The spatiotemporal dynamics of the OM along the estuary was investigated by comparing the bulk (elemental and isotopic composition) and structural (solid state C-13 nuclear magnetic resonance) features of the different pools of OM - dissolved OM (DOM), particulate OM (POM) and sediment OM collected during five sampling campaigns. Reverse osmosis coupled with electrodialysis (RO/ED) was used to concentrate and isolate DOM, yielding an average organic carbon recovery of 59% (+/- 15%). RO/ED had a limited effect on DOM properties, DOM showing > 75% of similarity with initial estuarine samples based on 3D fluorescence measurements. Bulk and structural analyses of DOM, POM and sedimentary OM showed that OM is mainly of aquatic origin in the Seine Estuary, regardless the OM pool. Nevertheless, significant differences in chemical composition between the three OM pools were observed: higher C/N ratios, carbohydrate, lipid and protein content as well as lower char and lignin contents in DOM than in the other two compartments. Spatial variations of OM properties, for POM and to a lesser extent DOM, were observed along the Seine Estuary based on delta C-13 and Delta C-14 analyses and C-13 NMR-derived protein and lipid contents, showing the transition from a riverine to a marine-dominated system. In the mixing zone of the estuary, the Delta C-14 composition of the sediment OM was related to the tidal strength, with strong tides leading to the resuspension of recent sediment OM and weak tides allowing the deposition of recent aquatic OM. Altogether, the combination of bulk and structural techniques showed that the Seine Estuary OM quality is mainly related to the compartment (DOM/POM/sediment) and to a lesser extent to the sampling zone (upstream/maximum turbidity zone/downstream). The approach proposed for the characterization of the Seine Estuary OM could be applied to other estuaries, allowing a better understanding of the complex OM dynamics in such ecosystems.