Brackish habitats are considered important for the facultatively catadromous European eel, but knowledge of eel habitat use strategies and the consequences on their condition, particularly in the estuaries areas, is limited and yet necessary for understanding some features such as growth and maturation in the different habitats that eel inhabit during the continental phase, that might also support assessment and management of local stocks, and contribute to the stock-wide assessment of this panmictic species. This study aimed to characterise and compare the condition of European eels according to their habitat use strategies and local estuarine characteristics. Eels were collected along the salinity gradient in six small and medium-sized estuaries located along the French coast in the eastern English Channel (i.e. the Slack, Wimereux, Liane, Canche, Authie and Somme estuaries). Four condition indices (i.e. Fulton condition factor K, lipid content, hepatosomatic index and health status) were measured on 119 individuals to explore variation with habitat characteristics at the small geographical scale and their habitat use strategies. Eel condition showed clear spatial differences between the six estuaries, with better condition in smaller estuaries. The spatial differences in eel condition appear to be related to variations in their diet composition, corresponding to different availability of macrozoobenthos prey among sites, in turn due to the local hydro-morpho-sedimentary characteristics. Environmental history and movements were reconstructed from the Sr:Ca and Ba:Ca ratios of otoliths from eel samples (N = 37) in both small- and medium-sized estuaries. The Sr:Ca and Ba:Ca ratios were used to distinguish the habitat use strategies and showed that both estuaries had a high proportion of resident eels (81%). Within each estuary, the Sr:Ca and Ba:Ca ratios were sufficiently contrasted to track movements of estuarine resident eels between three resident sectors (i.e. upper, middle and lower estuary). The relationship between eel condition and habitat use showed that inter-habitat shifter eels were in poorer condition than estuarine residents. Eel condition also varied between the three resident sectors, with decreases between eels from the lower to upper estuaries.