To determine whether thyroidal status is related to migratory and settling behavior in Anguilla anguilla glass eels, we sampled glass eels showing different migratory behaviors in the Arzal dam, which constitutes the tidal limit of the Vilaine River (France). We collected 4 groups of glass eels: flood and ebb tide glass eels were netted in the estuary during the flood and ebb tides, respectively, trap glass eels were sampled from the eel ladder trap, and bottom glass eels sheltering on the bottom of the estuary during flood tide. We measured individual whole-body triiodothyronine (T3) and thyroxine (T4) levels for these groups, and calculated total thyroid hormone (TH) levels as T3 + T4 contents reflecting the thyroid gland secretory activity, and T3:T4 ratios reflecting T4 outer-ring desiodase (T4 ORD) activity. Trap glass eels had the highest TH levels, indicating an activation of the thyroid gland via the thyreotrop axis. This could be responsible for the behavioral transition (loss of circatidal rhythm and switch to counter-current swimming) at the tidal limit and active colonization of river habitats by glass eels. Ebb and flood tide glass eels had similar TH levels that were lower than those of trap glass eels, indicating a lower thyroid gland secretory activity in the former. Ebb tide glass eels had higher T3:T4 ratios than flood tide and trap glass eels, indicating physiological stress related to inefficient use of tidal streams. Bottom glass eels had the lowest TH levels, and high T3:T4 ratios similar to those of ebb tide glass eels; this suggests that physiological stress induced by frequent counter-current swimming leads to precocious settlement of glass eels in estuarine habitats. Our data supports the critical role of the thyroid status in the migratory and settling behavior of glass eels in estuarine and marine habitats.