There is increasing evidence of water temperature being a key controlling factor of stream ecosystem metabolism. Although the focus of research currently lies on carbon emissions from fluvial networks and their potential role as positive climate feedback, it is also important to estimate the risk of eutrophication streams will be exposed to in the future. In this work, a methodological approach is developed to create a scientific basis for such assessment and is applied to two Austrian lowland rivers with significantly different characteristics. Gross primary productivity (GPP) is determined through the open diel oxygen method and its temperature dependence is quantified based on the metabolic theory of ecology. This relationship is combined with the outcomes of a climate change scenario obtained through a novel integrated modelling framework. Results indicate that in both rivers, a 1.5°C warming would provoke an increase of GPP of 7–9% and that such an increase would not be limited by nutrient availability. The results further suggest that the situation for the relatively shallow river might be more critical, given that its GPP values in summer are five times higher than in the deeper murky river.