Biogeochemical transformations of inorganic nutrients were studied in the mixing zone between the Danube and the north-western Black Sea in July 1995 and in the winter–spring transition period of 1997. Inorganic nutrients, phytoplankton carbon-biomass and biogenic silica were analysed at 10 different locations across the entire salinity gradient in combination with parallel measurements of phytoplankton carbon and inorganic nutrient uptake rates, making use of different tracers (14C, 15N, 32Si and 32P). The quantitative and qualitative nutrient signature of the Danube outflow into the Black Sea varied seasonally, depending on upwards processes of consumption, remineralization, transformation and elimination. Danube DSi (dissolved silicon) and DIN concentrations decreased from winter to summer, although PO4 remained constant for the whole season. The winter distribution of inorganic nutrients along the salinity gradient was conservative, and phytoplankton biomasses and activities were very low due to strong light limitation. However, significant phytoplankton carbon and inorganic nutrient uptake rates were measured in early spring and during summer at salinities depending on the hydrodynamics of the Danube and Black Sea mixing. Between a salinity of 0 and 10 (using the Practical Salinity Scale), phytoplankton (diatom) growth and mortality processes have been evidenced, which at first strongly lower the inputs of inorganic nutrients to the coastal zone, but also affect the balance among which nutrients are spread over the shelf. These modifications have important consequences for phytoplankton dynamics and species dominance at salinities above 10; diatom growth being apparently P-limited during spring and N-limited during summer. Surprisingly, no DSi limitation of diatom growth has been shown during this study, and a background DSi level of 2–3 μM was measured in the entire shelf area. Causes for such an observation appear to be (1) an efficient biotic and abiotic removal of PO4 during mixing, (2) an important denitrification in the upper estuary and (3) an important recycling of Si, both in the water column and at the sediment–water interface. The negative long-term effect of the quantitative and qualitative (deficiency in DSi) changes of the Danube inputs on the functioning of the Black Sea pelagic and benthic food-webs have been clearly reported in the literature and cannot be questioned by the present data set. Rather, this study simply highlights the complexity of the mechanisms by which propagation of the Danube eutrophication beyond the river plume possibly occurs.