The study of the dynamics of mollusc populations of the Saône and its two main tributaries, the Doubs and Ognon, over several years has provided us with the opportunity of highlighting the consequences of climatic warming and especially of the heatwave of 2003 on these organisms. From 1987 to 2003, the mean temperature of the waters of the Saône upstream of Lyon (Couzon) increased by 1.5°C. In addition, the summer of 2003 was the hottest since 1500 at least. We used correspondence analysis to identify structure change in mollusc data dating from September 1996 to December 2004. The results revealed: (1) during the period from September 1996 to July 2003, a significant progressive change in the mollusc community structure of the Saône upstream of Lyon, probably linked to the increase of temperature; (2) from July to August 2003 during the heatwave, a sudden change in the structure of mollusc communities and a significant decrease of species richness and density of gastropods and bivalves. During 2004, mollusc density and particularly that of Pisidium remained dramatically low. Similar observations were performed at four other sites along the Saône and in the lower reaches of its two main tributaries. This suggests that the resilience of the mollusc populations (i.e., the speed with which they return to a predisturbance state) to the heatwave is low. In this way, as different climatic models have predicted an increase in the frequency of summers as hot as that of 2003 during this century, more than half the mollusc species currently inhabiting the potamic area of the Saône, Doubs and Ognon, and probably other large rivers, are probably directly threatened with extinction.