There is a lack of information on many biological and ecological aspects of the critically endangered European eel during its growth phase in inland waters, such as when the sedentary life stage begins, mobility according to age and response to habitat alteration. We used mobile radio frequency identification (RFID) telemetry technology to track tagged eels over 6 years after their restocking as glass eels in six typologically different rivers. We also cross-referenced telemetry data with those of several electrofishing monitoring sessions to better understand the mobility and behaviour of eels. The relative abundance (maximum 52 individuals km−1) and detection rate (maximum 28%) of eels were not significantly correlated with the time/age after restocking. Eels were present in all restocked rivers, but their abundance was low and mobility was high in a slightly acidified, oligotrophic river that had experienced a great loss of fish habitat heterogeneity. This loss of habitat heterogeneity was due to flooding events and machinery works in riverbeds to restore the altered riverbanks. Four years after glass eel release, restocked eels became sedentary and moved from shallow to deep microhabitats with riverbeds dominated by blocks as the bottom substrate. After this age, they exhibited high fidelity to the residence site. This study provides new insights concerning the biology and ecology of eels restocked as glass eels in freshwaters, which should lead to improved management plans for the species through the implementation of more effective conservation measures and strategies.