The research presented in this special issue of the Journal of Hydrology is brought together with associated information of relevance to the thematic area in this concluding paper. Some of the important gaps in our current knowledge are outlined with a view to identifying future research needs for the development of an integrated analysis of nutrients in river basins and their management. Identification of these needs is important if we are to meet the defined set of catchment management objectives specified under the EU Water Framework Directive that must be delivered against a specified timetable. The Directive raises wider concerns such as how to define ‘good ecological status’ and pertinent to this special issue: what role nutrients have in framing this definition. In this paper, the importance of nutrient pressures on receiving waters is evaluated in the context of the key scientific uncertainties and options for characterising the biological, physico-chemical and hydro-morphological parameters necessary to meet the science needs of the Directive. An assessment of the significance of nutrient mobility within river basins for current understanding of freshwater systems functioning on a catchment and basin scale is made together with an evaluation of where research on nutrient pressures should be focussed in order underpin effective management.