Human activities increasingly threaten the highly biodiverse freshwater ecosystems. Life Cycle Assessment (LCA) is a useful tool to quantify the impacts of products and services on freshwater biodiversity. Current methodologies in LCA address the impact of climate change on freshwater fish diversity by changes in average river discharge only. Given the ectothermic nature of fish, previous studies have highlighted the importance of including water temperature changes as a driver of species loss. Moreover, the impact of climate extremes might be more important than changes in average conditions. In this study, we derived new characterization factors for 207 individual greenhouse gas (GHG) emissions that quantify the impact of an emission change on freshwater fish, accounting for climate-driven changes in both streamflow and water temperature extremes. We combined a novel dataset of fish range climate threats with a newly developed species-area relationship to quantify global freshwater fish extinction risks at various global warming levels. The global characterization factors range from 0.00 to 4.56·10−10 Potentially Disappeared Fraction (PDF)·yr·kg−1. Our results imply that freshwater fish diversity impacts per kg of GHG emission have been underestimated in previous LCA methods that excluded the impact of water temperature and climate extremes, as the newly developed effect factor is higher by 172%. Future contributions should focus on increasing taxonomic coverage (e.g., by including lentic fish species and macro-invertebrates) and developing complementary models to reflect other aspects of biodiversity in LCA.