jats:pWe investigated carbon isotopic ratios (δ13C) v. carbon to nitrogen (C : N) ratios for surface sediments throughout a large estuarine system (Río de la Plata, RdlP), combined with sediment cores from adjacent marshes to infer main carbon sources. We also evaluated the influence of the El Niño–Southern Oscillation (ENSO) and associated high freshwater-discharge events on the organic-matter transport within the estuary. The isotopic pattern in surface sediments of the RdlP showed the upper reaches to be influenced by riverine particulate matter (δ13C range: –24 to –26‰). Similarly, in the sediment cores from marshes of the upper reaches, δ13C values decreased from –24‰ in ancient sediments to –28‰ in recent sediments, reflecting an increased contribution of organic matter from land, including C3 plants and freshwater phytoplankton, during the past 50 years. However, the lower reaches represent a depositional environment of marine algae (δ13C range: –21 to –23‰), with no influence of detritus from adjacent marshes, indicating minor erosion of the marshes in the lower reaches operating as carbon-sink habitats. Our isotopic analysis showed that the transport and deposition of terrigenous organic matter within the RdlP and adjacent marsh habitat appear to be both temporally and spatially linked to hydrology patterns.</jats:p>