Sea-bass (Dicentrarchus labrax) grow under different salinity regimes, from the open sea to lagoons and even rivers, but some mortality has been recorded in juvenile stages when exposed to low salinity water. Changes in water permeability of different osmoregulatory tissues could be the cause of reduction in blood osmotic pressure and death in some fish in fresh water (FW). In order to explore this condition, we have studied the changes of aquaporins (AQP1 and AQP3), alpha1 and alpha4 Na(+)/K(+)-ATPase transcript levels in the digestive tract, kidney and gills after a long-term exposure of juvenile sea-bass to sea water (SW) and FW fish able to survive in SW and FW are called SW-adapted fish (SWS), FW successfully-adapted fish (FWS) respectively, while fish that die in FW are called FW unsuccessfully-adapted fish (FWU). AQP1 was highly expressed in SWS digestive tract and kidney, suggesting its involvement in water absorption. In FWU, AQP1 transcript levels in the digestive tract were higher than in FWS, suggesting higher water absorption. AQP3 transcript levels in gills were higher in FWS compared to SWS, suggesting a role in FW adaptation. AQP3 transcript levels in gills were higher in FWU than in FWS, suggesting an increase in gill water permeability or other solutes. Transfer to FW was followed in gills by an increase in alpha1 and alpha4 Na(+)/K(+)-ATPase levels in FWS and FWU, supporting the current model of ion absorption through the gills.