The Gironde is the largest estuary of South-West Europe and is one of the best monitored estuarine systems in the world. This macrotidal estuary is characterized by a low biodiversity in both oligo- and mesohaline zones. Its zooplankton community is constituted by only five major species, three calanoid copepods (including one invasive species) and two mysids. Retrospective analyses have already documented a warming associated to a phenomenon of marinisation. Here, we investigate the influence of both marinisation and warming on the spatial distribution and the abundance of copepods (i.e. Eurytemora affinis, Acartia bifilosa and neritic species) in the Gironde estuary. We modelled the environmental envelope of the copepods as a function of salinity and temperature to demonstrate that the alteration of their longitudinal distribution in the estuary between 1975 and 2003 was the result of both changing temperature and salinity. Although the upstream movement of neritic species was mostly related to salinity, we show that the augmentation of both temperature and salinity was at the origin of the upstream progression of both A. bifilosa and E. affinis. These results suggest that the distribution of copepods can be affected by both anthropogenic forcing and climatic change, which modulate the physic-chemistry of the Gironde estuary.