Uptake of dissolved ammonium, nitrate, nitrite, urea and amino acids was studied in the Scheldt estuary in different seasons over a salinity gradient. The importance of inorganic nitrogen sources was compared to that of urea and amino acids and the relative use of urea and amino acid nitrogen and carbon was studied. Urea and amino acids constituted up to 43 and 29% of total nitrogen uptake, respectively, and were of similar importance as inorganic substrates. Ammonium oxidation by nitrifiers and ammonium uptake by algae and bacteria were of similar magnitude. In January, April and November, amino acids constituted a source of both nitrogen and carbon while urea mainly constituted a source of carbon. During the summer months, amino acids were used mainly as a source for nitrogen, while urea was a source for both carbon and nitrogen; urea was rarely used as nitrogen substrate alone. Due to this seasonal uncoupling of nitrogen and carbon assimilation, dually labeled substrates are necessary to assess the importance of urea and amino acids as substrates for organic nitrogen and carbon.