Groundwater inflow can be a significant source of nutrients for riverine ecosystems, which can affect eutrophication i.e., the elevated primary production and the corresponding accumulation of algal biomass. Experimental and modelling work has shown that benthic algae (autotrophic biofilms) in particular benefit, as they have direct access to the inflowing groundwater-borne nutrients. Primarily the supply of phosphorus (P) enhances pelagic algal biomass, as it is the limiting nutrient for primary production in most freshwater systems. In this study, we estimate the effect of groundwater inflow on overall eutrophication of a large, European lowland river and tested its seasonal effect on biofilms in particular. We calculated the effects on overall eutrophication during summer according to the estimated input of groundwater-borne P and the C:P stoichiometry of planktonic algae in the Elbe River. Our model indicated that these diffuse P inputs have the potential to significantly increase eutrophication. Groundwater-P can contribute up to 1.5 t/d PO4 over the investigated 450 km stretch of the Elbe River under low flow conditions. This would result in an additional planktonic load of about 46 t/d of particulate organic carbon, thereby contributing to eutrophication at the regional scale in this river. In contrast, at the local scale, biofilms were collected seasonally from artificial substrata exposed in the river either in hydrogeologically active areas with groundwater inflow, or in areas of varying hydraulic connectivity. Analyses of biofilm macronutrients, structural components and biofilm community composition show distinct effects of season, hydrogeology and groundwater inflow. The dominant predictors were season and the interaction between hydrogeology and groundwater. Benthic eutrophication is most likely to occur in autumn in areas of loose rock with high groundwater inflow. The strong interaction of environmental factors in determining benthic eutrophication highlights the need to assess these factors in combination rather than in isolation.