Abstract The EU WFD requires an integrated approach to river basin management in order to meet environmental and ecological objectives. This paper presents concepts and full-scale application of an integrated modelling framework. The Ringkoebing Fjord basin is characterized by intensive agricultural production and leakage of nitrate constitute a major pollution problem with respect groundwater aquifers (drinking water), fresh surface water systems (water quality of lakes) and coastal receiving waters (eutrophication). The case study presented illustrates an advanced modelling approach applied in river basin management. Point sources (e.g. sewage treatment plant discharges) and distributed diffuse sources (nitrate leakage) are included to provide a modelling tool capable of simulating pollution transport from source to recipient to analyse effects of specific, localized basin water management plans. The paper also includes a land rent modelling approach which can be used to choose the most cost effective measures and the location of these measures. As a forerunner to the use of basin scale models in WFD basin water management plans this project demonstrates potential and limitations in comprehensive, integrated modelling tools.