This paper introduces a new approach to the modelling of interdisciplinary river catchment management, a project for the management of watersheds being conducted at the UFZ Environmental Research Centre. The new European Union Water Framework Directive shifts the management of water resources beyond political boundaries (e.g. state, country) to focus on the total river catchment area. The project currently incorporates the following components: hydrology, sediment and nutrient transport, wetland research, river water quality, ecotoxicology, socio-economics and decision making. A river basin management tool is in the process of being developed, based on basic research in different landscape compartments (e.g. running waters, catchment area). Thus, rehabilitation measures in different landscape compartments can be evaluated, and interactions and dependencies between these components along the river reach can be included in the assessment process. The integrated management tool consists of several hydrological and biological computer models which are linked in an object orientated way. Each model and its input and output flow is controlled via a GIS interface. Special emphasis is placed on the development of specific regionalization procedures. Modularity is a key feature of the system, allowing each model to be run as a stand-alone model. An additional important feature of the system is it’s flexibility in allowing models to be added or removed to fit project requirements.