Study region: Our study region extends over 450 stream km of the German part of the Elbe River, an ecologically and economically important first order river, between Schöna and Wittenberge. Study focus: Diffuse groundwater born nutrients are major contributors to increased algae growth in rivers, leading to eutrophication with serious consequences for water quality and ecosystem health. Therefore, knowledge of the spatial and temporal dynamics of diffuse groundwater discharge are required since groundwater often remains as a ‘black box’ for the identification of nutrient sources by managers. The multi-method approach, based on the inverse geochemical and tritium modelling, a flux balance, a darcy approach and hydraulic gradients, showed complex spatiotemporal dynamics along the studied reach of the Elbe River. Groundwater inflow was variable but occurred along the entire river. Areas of high groundwater fluxes were located in the upstream mountainous catchment areas and decreasing downstream. New hydrological insights for the region: The multi-method approach provides a blueprint for the assessment of other large river systems. No single method was able to create conclusive results and most other approaches are only applicable in smaller stream systems. First time an estimation of groundwater flux rates, that can be used to quantify matter inputs, was made. In addition, we showed a way to detect and assess the impact of drainage channels in a heterogenous river system.