Although the average growth rate of European eel is known to be generally dependent on temperature and habitat at the population scale, large variation in growth among eels in a single river basin can also be widely observed. In this study, individual growth trajectories of female European eels in the Gironde River basin, France, were modeled with habitat-use histories and thermal variations in relation to regional climatic events such as the heat wave in 2003 observed in SW Europe. A mixed-effects model was used to take into account the repeated measures of individual growth of 173 female eels in 1993 to 2003, obtained from otolith structure and chemistry. Temperature effect was tested using a proxy of efficient temperature for growth between 2 thermal thresholds in a year. The models with thresholds for growth between 12 and 15°C (lower) and 18°C (higher) were selected considering Akaike’s information criterion. Individual annual growth estimates were higher in the estuary habitat than in the river habitat. Estimated growth was higher when eels shifted habitats between freshwater and brackish water or seawater. The years 1999 and 2001 had, respectively, the lowest and highest temperature proxy value, showing that a longer growing season (moderate summer/warm winter) had a positive effect on growth. The 2003 heat wave had a negative effect on eel growth, reflected by the lower temperature proxy value. The same approach could be used in the future to estimate the effect of global climate change on the growth and distribution of eels at local and regional scales.