We analyzed a 10-m sediment core retrieved at 82 m water depth off the coast of the Tagus River (Western Iberian Margin, Portugal) to investigate a linkage between variations in benthic foraminiferal assemblages and Tagus River discharge over the last 5700 years. Benthic foraminiferal assemblages were studied at high resolution in combination with the stable carbon and oxygen isotopic composition of fossil shells of Nonion scaphum, bulk and molecular organic matter properties (TOC, TN, C/N ratio, delta C-13(TOC), delta N-15(bulk), and BIT index), magnetic susceptibility, and XRF analyses. Three periods of environmental changes were identified: 1) high Tagus River discharge in 5750-2200 calendar year before present (cal yr BP), 2) lower discharge characterized by intense upwelling conditions (2250-1250 cal yr BP), and 3) both intense upwelling and Tagus River discharge (1250 cal yr BP-present). The data reveal alternating intense upwelling periods, as shown by the dominance of Cassidulina carinata, Valvulineria bradyana, or Bulimina marginata, whereas periods of increased river discharge are indicated by increase of N. scaphum, Ammonia beccarii, and Planorbulina mediterranensis. The Tagus River discharge was the strongest during the first period, transporting riverine material further offshore and preventing the establishment of a mud belt on the mid-shelf (around 100 m depth). During the second period, a decrease in Tagus River discharge favored the formation of the Tagus mud belt and strongly influenced the benthic environment by creating an organic matter stock. During the third period, intense upwelling and increased Tagus River discharge were recorded by benthic foraminiferal distribution, with an increase of terrestrial elements present in the mud belt. Furthermore, our results showed that variations in benthic foraminiferal assemblages corresponded to the well-known climatic periods in the study area, such as the Roman Period, the Dark Ages, the Medieval Warm Period, and the Little Ice Age. Our study strongly suggests that benthic foraminiferal assemblages can be used as a bio-indicator to trace the influence of past river discharge.