In the context of climate change and food provisioning for a growing global population, the impacts of water consumption on aquatic biodiversity (e.g., river water consumption for irrigation) should be considered in Life Cycle Impact Assessment (LCIA). A previous LCIA method quantifying the potential impacts of river water consumption on fish biodiversity, using a species-discharge relationship (SDR), constituted an essential first step. This method is however limited in terms of regionalization and taxa considered, and predicts the potential risk of local species loss only. Here, we address these shortcomings by developing region-specific SDRs for Europe at various scales (continent, country, and eco-region), and including macro-invertebrate biodiversity. SDR exponents vary from 0.06 to 0.45 between regions, underlining the importance of such regionalization. Furthermore, we provide a new regionalized method which considers the location of water consumption within a river basin, by integrating the concept of longitudinal river zonation. This involves the use of a novel measure of potential loss of species richness, standardizing local species loss to an equivalent of global extinction and reflecting species vulnerability. The new method is applied in a Swiss case-study. The consideration of the location of water consumption within a basin was found to be of high importance in the assessment: potential species loss varied between 4.22 × 10(-3) and 3.95 × 10(-1) species (2 orders of magnitude) depending on location. This work thus provides enhancements in the assessment of potential impacts of river water consumption on aquatic biodiversity and contributes to the ecological relevance of the method.