The efficiency of glass eel restocking as a conservation measure to restore the altered local eel stocks has never been evaluated by integrating the dimension of typological diversity of freshwater habitats in eel recruitment performance in terms of the abundance, density, growth, silvering, survival, catchability and eel yields. Here, we used the electrofishing method during a 6-year study to catch eels, and the most appropriate Jolly–Seber model was applied to estimate the demographic parameters in open populations. We found that most eels were yellow eels in the growth phase with a low abundance (eels 3⁺: 2.8% and eels 5⁺: 7.1%) of silver eels, which were only males at the MII migrating phase. Eel recruitment performance varied between sector/river habitats. Restocked eels showed annually positive allometric growth type with good length increments and better condition factors. They have survived in almost all sectors with a survival rate > 0.810. Eels were more abundant and denser (maximum 0.128 individuals m⁻²) in one sector with a high quality of habitats offering optimal living conditions in terms of the protection against predators and water flow, settlement and food availability, as revealed by it having the highest eel yields. In contrast, no eels were found in two sectors whose habitats offered a high threat of predation, poor burial properties and insufficient protection against water flow. Sector/river habitats play a key role in the success of yellow eel production and certainly, over time, future genitor production. This study provides recommendations for the management of eels and their habitats during restocking aimed at the conservation of this threatened species.