High-resolution diatom and phytolith quantitative and assemblage analyses have been conducted on two box-cores from the Tagus pro-delta (SW Portuguese Margin) in order to compare these common palaeoceanographic proxies to instrumental data describing the upwelling regime and the freshwater input of the Tagus River. The western Portuguese margin is affected by seasonal coastal upwelling controlled by northerly winds and by strong freshwater input through the Tagus River, which is controlled by precipitation over the whole Iberian Peninsula. For both upwelling and freshwater input, instrumental data such as river flow and an upwelling index, are available for the last ~100 and 50 yr, respectively. Diatoms and phytoliths are used as proxies for salinity and productivity changes, resulting from river input and upwelling variability. Comparison of the proxy and instrumental records confirms that diatom abundance and, in particular, the genus Chaetoceros (Ehrenberg) traces the main periods of intense upwelling, whereas freshwater diatoms and phytoliths trace the major floodings of the Tagus River. The results confirm that, despite the dissolution affecting silica compounds in the water column and in the sediment, diatoms and phytoliths are an accurate recorder of upwelling events and river discharge in this area. Based on such verification, the proxies can be used to reconstruct palaeoenvironments on timescales reaching far beyond the range of instrumental data.