The Danube Water Quality Model (DWQM) was developed in the framework of the GEF project “Danube River Basin Pollution Reduction Programme” (1999) and updated in a large international research project called “Nutrient Management in the Danube Basin and its Impact on the Black Sea” (acronym daNUbs, 2001–2005). The DWQM simulates the water quality in the Danube River and its main tributaries as a function of space and time, dependent on the river morphology and hydrology and on emissions calculated by the model MONERIS. The specific goal of the DWQM is to simulate the nutrient loads to the Black Sea in support to the management of the nutrients nitrogen (N) and phosphorus (P) in the Danube River Basin and to distribute them over time and over the different nutrient species. Both distributions are decisive for the assessment of the impact of the Danube outflow on the north-western shelf of the Black Sea. This chapter discusses the set-up of the DWQM and its application to the conditions around the year 2000, which served both to enhance our understanding and to calibrate and validate the DWQM. The validated DWQM has been used to assess five scenarios for future management alternatives, varying from “business as usual” to “deep green”. Where appropriate, we refer to the underlying scientific papers and reports.