Fine sediment transport in rivers is exacerbated during flood events. These particles may convey various contaminants (i.e. metals, pathogens, industrial chemicals, etc.), and significantly impact water quality. The exceptional June 2016 flood of the Seine River (catchment area: 65 000 km², France), potentially mobilized and deposited contaminated materials throughout the Paris region. Flood sediment deposits (n = 29) were collected along the Seine River and its main tributaries upstream (Yonne, Loing and Marne Rivers) and downstream of Paris (Oise and Eure Rivers). Fallout radionuclides (¹³⁷Cs, ⁷Be) were measured to characterize the sources of the material transiting the river, while trace elements (e.g. Cr, Ni, Zn, Cu, As, Cd, Sb, Pb, Tl, Ag) and stable lead isotopes (²⁰⁶Pb/²⁰⁷Pb) were analyzed to quantify the contamination of sediment transported during the flood. In upper sections of the Seine River, sediment mainly originated from the remobilization of particles with a well-balanced contribution of surface and subsurface sources. In the upstream tributaries, sediment almost exclusively originated from the remobilization of subsurface particles. In Paris and downstream of Paris, recently eroded particles and surface sources dominated, suggesting particles were mainly supplied by urban runoff and the erosion of agricultural soils. The highest metal concentrations and Enrichment Factors (EF) were found in the sediment collected in the Loing, Orge and Yvette upstream tributaries. Although these inputs were diluted in the Seine River, an increase in elemental concentrations was observed, progressing downstream through Paris. However, EFs in sediment collected along the Seine River were lower or in the same range of values sampled over the last several decades, reflecting the progressive decontamination of the urbanized Seine River basin.