The assessment of the impacts of climate change on freshwater biodiversity lags far behind those on terrestrial and marine systems despite the vulnerability and importance of freshwaters to humans. Here we introduce a new project aiming at combining statistical hydrological and ecological models with empirical approaches to produce a comprehensive assessment of the risks of climate warming to freshwater biodiversity across representative river networks in Japan. Currently in its first year, we focus on the initial phase of the project consisting on the establishment of air and water temperature monitoring networks in target catchments and the subsequent development of statistical models for prediction of stream water temperatures. Preliminary results using linear regression models show acceptable prediction performance of daily average temperatures in the monitored streams, suggesting good scope for improvement in the following years of the project as more data become available and we test more complex models.