There is increasing evidence that the global climate change is already having measurable biological impacts. However, no study (based on actual data) has assessed the influence of the global warming on communities in rivers. We analyzed long-term series of fish (1979–1999) and invertebrate (1980–1999) data from the Upper Rhône River at Bugey to test the influence of climatic warming on both communities. Between the periods of 1979–1981 and 1997–1999, the average water temperature of the Upper Rhône River at Bugey has increased by about 1.5°C due to atmospheric warming. In the same period, several dams have been built from 12.5 to 85 km upstream of our study segment and a nuclear power plant has been built on it. Changes in the community structure were summarized using multivariate analysis. The variability of fish abundance was correlated with discharge and temperature during the reproduction period (April–June): low flows and high temperatures coincided with high fish abundance. Beyond abundance patterns, southern, thermophilic fish species (e.g. chub, and barbel) as well as downstream, thermophilic invertebrate taxa (e.g. Athricops, Potamopyrgus) progressively replaced northern, cold-water fish species (e.g. dace) and upstream, cold-water invertebrate taxa (e.g. Chloroperla, Protoneumura). These patterns were significantly correlated with thermal variables, suggesting that shifts were the consequences of climatic warming. All analyses were carried out using statistics appropriate for autocorrelated time series. Our results were consistent with previous studies dealing with relationships between fish or invertebrates and water temperature, and with predictions of the impact of climatic change on freshwater communities. The potential confounding factors (i.e. dams and the nuclear power plant) did not seem to influence the observed trends.