Eels colonize either marine, estuarine or freshwater habitats, with marine and estuarine eels tending to grow faster than freshwater eels. The reasons for these divergent migratory tactics and growth trajectories remain poorly understood. In order to investigate the role of salinity preferences of glass eels in the control of habitat selection and growth plasticity, we sorted different contingents of glass eels Anguilla anguilla through 2 consecutive salinity preference tests. This allowed us to study the link between salinity preference and locomotor activity (i.e. positive rheotaxis), and to distinguish contingents of glass eels that were either plastic or fixed in their preference for freshwater (FW) or saltwater (SW). Subsequently, we monitored somatic growth of the different contingents in controlled SW and FW rearing conditions. Preference for FW was linked to high locomotor activity, a behavioral pattern likely to promote colonization of FW habitats in the wild. Accordingly, FWC (FW contingent, i.e. glass eels that preferred FW twice) exhibited poor growth, similar to those observed in wild FW eel populations. In contrast, preference for SW was linked to low locomotor activity, and the SWC (SW contingent, i.e. glass eels that preferred SW twice) had high growth rates in SW, as observed in wild marine and estuarine populations. The PCC (plastic contingent, i.e. glass eels that swappped their salinity preference) had an intermediary growth status that could be related to the ‘nomad' life style of eels migrating between different habitat types during their life. Growth was significantly higher in SW compared to FW in all contingents, indicating that habitat salinity may directly affect growth, irrespective of food availability. Our results demonstrated that glass eel salinity preference was linked to their locomotor activity and growth performance, and provided a comprehensive ecological mechanism for the control of habitat distribution and growth patterns observed in wild eel populations.