Episodic acidification resulting in increased acidity and inorganic aluminum (Al(i)) is known to interfere with the parr-smolt transformation of Atlantic salmon (Salmo salar), and has been implicated as a possible cause of population decline. To determine the extent and mechanism(s) by which short-term acid/Al exposure compromises smolt development, Atlantic salmon smolts were exposed to either control (pH 6.7-6.9) or acid/Al (pH 5.4-6.3, 28-64 microgl(-1) Al(i)) conditions for 2 and 5 days, and impacts on freshwater (FW) ion regulation, seawater (SW) tolerance, plasma hormone levels and stress response were examined. Gill Al concentrations were elevated in all smolts exposed to acid/Al relative to controls confirming exposure to increased Al(i). There was no effect of acid/Al on plasma ion concentrations in FW however, smolts exposed to acid/Al followed by a 24h SW challenge exhibited greater plasma Cl(-) levels than controls, indicating reduced SW tolerance. Loss of SW tolerance was accompanied by reductions in gill Na(+),K(+)-ATPase (NKA) activity and Na(+),K(+),2Cl(-) (NKCC) cotransporter protein abundance. Acid/Al exposure resulted in decreased plasma insulin-like growth factor (IGF-I) and 3,3',5'-triiodo-l-thyronine (T(3)) levels, whereas no effect of treatment was seen on plasma cortisol, growth hormone (GH), or thyroxine (T(4)) levels. Acid/Al exposure resulted in increased hematocrit and plasma glucose levels in FW, but both returned to control levels after 24h in SW. The results indicate that smolt development and SW tolerance are compromised by short-term exposure to acid/Al in the absence of detectable impacts on FW ion regulation. Loss of SW tolerance during short-term acid/Al exposure likely results from reductions in gill NKA and NKCC, possibly mediated by decreases in plasma IGF-I and T(3).