Résumé : The ecological model BIOGEN, describing the carbon, nitrogen, phosphorus and silicon cycling throughout aggregated chemical and biological compartments of the planktonic and benthic marine systems, has been implemented in the north-western Black Sea to assess the response of this coastal ecosystem to eutrophication by the Danube River. The trophic resolution of BIOGEN was chosen to simulate the major ecological changes reported in this coastal area since the 1960s. Particular attention was paid to establishing the link between quantitative and qualitative changes in nutrients, phytoplankton composition and food-web structures. The BIOGEN numerical code structure includes 34 state variables assembled in five interactive modules describing the dynamics of (1) phytoplankton composed of three distinct groups, each with a different trophic fate (diatoms, nanophytoflagellates, non-silicified opportunistic species); (2) meso- and microzooplankton; (3) trophic dead-end gelatinous organisms composed of three distinct groups (the omnivorous Noctiluca and the carnivores Aurelia and the alienMnemiopsis ), and organic matter degradation and associated nutrient regeneration processes by (4) planktonic and (5) benthic bacteria. The capability of the BIOGEN model to simulate the recent ecosystem changes reported for the Black Sea was demonstrated by running the model for the period 1985–1995. The BIOGEN code was implemented in an aggregated and simplified representation of the north-western Black Sea hydrodynamics. The numerical frame consisted of coupling a 0-D BIOGEN box model subjected to the Danube with a 1-D BIOGEN representing the open-sea boundary conditions. Model results clearly showed that the eutrophication-related problems of the north-western Black Sea were not only driven by the quantity of nutrients discharged by the Danube, but that the balance between them was also important. BIOGEN simulations clearly demonstrated that phosphate, rather than silicate, was the limiting nutrient driving the structure of the phytoplankton community and the planktonic food-web. In particular, it showed that a well-balanced N:P:Si nutrient enrichment, such as that observed in 1991, had a positive effect on the linear, diatom–copepod food-chain, while the regenerated-based microbial food-chain remained at its background level. When present, the gelatinous carnivores also benefited from this enrichment throughout their feeding on copepods. A synergetic effect of fishing pressure and cultural eutrophication was further indirectly suggested by modifying the mortality coefficient of copepods. However, BIOGEN scenarios with unbalanced nutrient inputs, such as nitrogen or phosphate deficiency recorded in 1985 and 1995, predicted the dominance of an active microbial food-web in which bacteria and microzooplankton played a key role; the former as nutrient regenerator, the latter as a trophic path to the copepods and hence to the carnivorous. In such conditions, however, a significant biomass reduction of all gelatinous organisms was simulated, in perfect agreement with recent observations. From these model scenarios it is suggested that the observed positive signs of Black Sea ecosystem recovery might well be related to the reduction of nutrient loads in particular phosphate, by the Danube.