We investigated long‐term trends (1965–2002) in dissolved inorganic nutrients in the tidal part of the Scheldt estuary (Belgium, The Netherlands). Annually averaged concentrations of dissolved silicate (DSi), dissolved inorganic nitrogen (DIN), and phosphate (DIP) increased significantly until the mid‐1970s, after which they declined linearly at rates of 0.6, 2.9, and 0.3 µmol L ‐ yr ‐ , respectively. This co‐occurred with a deterioration followed by a restoration of water column oxic conditions. Because of the differences in the reduction rate of DSi (1.2% yr ‐ ), DIN (1.7% yr ‐ ), and DIP (5.4% yr21), the N: P and Si : P ratios more than doubled from 1980 to 2002. The Si :N ratio varied from 0.2 to 0.4 and was positively correlated with river discharge. The part downstream from the confluence of the main rivers was a net sink for DSi during the entire period but evolved from a net sink to a net source for DIP, while the reverse was true for DIN. This differential behavior of the estuary with respect to DIN and DIP strongly buffered the altered loadings to the upper estuary. The input of oxygen‐consuming substances at the head of the estuary triggered a sequence of oxidation reactions. In the early 1970s, high loadings of ammonium and organic matter caused oxygen depletion and intense water‐column denitrification in the upstream part and intense nitrification downstream, with a nitrate maximum succeeding a nitrite peak. With oxic conditions improving and the input of ammonium decreasing, water‐column denitrification declined, the nitrification front migrated upstream, and the estuary evolved from a net producer of nitrite to a net consumer. Now, at the beginning of the 21st century, nitrate behaves almost conservatively over the entire estuary.