Abstract The nitrogen signature of marginal ice zones in the Southern Ocean often departs from the “classical” Antarctic nutrient profiles with high nitrate and low ammonium values in the surface layer. Weddell Sea marginal ice zones e.g. show enhanced nitrate depletions, amounting to ~ 500 mmol N m−2. Additionally, ammonium stocks in the upper layer can be up to 7% of the inorganic nitrogen pool. The corresponding nitrogen uptake regime suggests elevated nitrate assimilation during the early phase of the productive season and significantly reduced nitrate assimilation at a later stage. Absolute as well as specific nitrate uptake rates decrease by an order of magnitude when ammonium stocks exceed 1.7% of the total inorganic nitrogen. The variability in nitrogen utilisation reflects physiological changes in the phytoplankton assemblage. In response to increased ammonium stocks phytoplankton show a reduction in their capacity to take up nitrate and following an initial diatom bloom non-siliceous phytoplankton become predominant in a regenerated production regime.