Eel aquaculture is capture based and thus dependent on the fishery for juvenile glass eels. This fishery typically takes place in estuaries where salinity varies and ammonia levels can be elevated. Also, during capture and transport glass eels are kept at high densities and ammonia from endogenous production can increase to toxic levels. Ammonia is known to have detrimental effects on fish growth and survival. In the present study, the salinity dependence of ammonia sensitivity in glass eels acclimated to either seawater or freshwater was determined, and the possible role of branchial sodium/potassium adenosine triphosphatase (Na+/K+ -ATPase) was investigated. Freshwater-acclimated glass eels were found to be more sensitive to ammonia with a lethal concentration to 50% of the test organisms (LC50) value for 96 h of 3.30 mM for total ammonia nitrogen (TAN) and 117 microM for un-ionized ammonia (UIA), versus values of 4.95 mM and 138 microM, respectively, for seawater-acclimated animals. Freshwater glass eels also had significantly lower body TAN levels than seawater-acclimated glass eels, although body accumulation profiles during exposure were similar. The higher branchial Na+/K+ -ATPase activities in seawater glass eels might explain this difference in sensitivity; however, activities decreased significantly with increasing ammonia levels. There was also no salinity dependence of net ammonia flux rates (0.388 micromol of TAN/g/h). Holding glass eels at high densities characteristic of transport conditions resulted in elevated ammonia concentrations to approximately 3 mM, which coincidently approaches to the freshwater LC50 value and may therefore contribute to mortality.