The European sturgeon (Acipenser sturio) is a critically endangered anadromous fish species with the last remaining population living in the Gironde estuary, thanks to restocking programs. Between 2010 and 2018, trawling surveys (1022 trawl tows) in the estuary caught 452 sturgeons (fork length (FL) from 25.5 cm to 154 cm). Based on previous knowledge about the species ecology, individuals have been categorized into two groups, Estuarine Dwellers (ED; FL below 68 cm) that are using mainly the estuary, and Sea Explorers (SE; FL equal or above 68 cm) that could accomplish migration at sea. ED and SE were found in the estuary at all seasons with densities being the highest in autumn for SE and in all season except spring for ED. Hotspot analyses were made at the seasonal scale to localise ED and SE concentrations. Differences were analysed according to environmental variables (temperature, water column height, salinity and concentration in suspended matters) extracted from a hydrodynamic model (MARS3D), which all contribute to fish localisation at all seasons. In all seasons, both groups were using common areas located downstream (overlap from 26 to 33%) except in autumn, when different areas were used (12% overlap). SE were encountered downstream in deeper areas with higher salinity and lower temperature (except in winter). For this group, temperature seems to be a limiting factor. ED occupied downstream as well as upstream areas with lower salinity and higher temperature in summer, but there was no habitat selection linked to simulated environmental variables in spring and autumn. Since ED are mainly using the estuary they are probably accustomed to the range of values of the abiotic variables characterising the estuary and other factors are probably at play in spring and autumn, such as prey distribution. Comparison with the location of ancient wild cohorts highlights common hotspot areas downstream with our stocked population but the disappearance of a former upstream hotspot. We explained this difference by the environmental changes witnessed by the estuarine environment in the last decades. Our results highlights important areas for both groups that could help the design of conservation measures.