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A combined analysis of sedimentological, molecular, and microfossil proxies was used to determine paleoclimatic and paleoceanographic variations and assess sediment transport pathways along the last c.a. 6300 years in a sedimentary record collected on the inner shelf of the southwestern Atlantic Ocean. The combined use of terrestrial and marine proxies enables a more complete environmental perspective of the La Plata River plume influence on the southwestern Atlantic shelf, regarding the relationship between climate, productivity, as well as hydrodynamic. Variations in marine productivity, lipid biomarkers of terrestrial plants, diagnostic geochemical indices, and sea-surface temperature point to three phases within the core. The first interval (6300–5200 cal yr BP) was characterized by low marine and terrigenous organic matter input, with pulses of phytodetritus indicated by benthic foraminifera. These features suggested dry climatic conditions over the southeastern portion of South America, with the influence of sediments from the adjacent continent and, on a smaller scale, transported from the Argentinian shelf due to the high relative sea level. The second interval (5200–2800 cal yr BP) was distinguished by a slight increase in marine productivity and terrigenous input, indicating a transition period with an increase of total rainfall influenced by an intensified South American Monsoon System (SAMS) and the modern El Niño-Southern Oscillation (ENSO) phenomenon. These features, associated with the changes in wind patterns and the lower relative sea level, suggest the onset of the influence of the La Plata River (LPR) plume over the southern regions of the Brazilian continental shelf for the last 6300 cal yr BP. The last interval (2800–890 cal yr BP) had the highest contents of marine and terrigenous proxies, suggesting less climatic variability, as the long-term intensification of the SAMS and a further increase in the amplitude of the ENSO resulted in the modern establishment and dominant influence of the LPR plume on the core site. Variations in sea-surface temperature up to 3.3°C were related to the influence of the LPR plume on the shelf off southern Brazil.