Episodic stream acidification from atmospheric deposition is suspected to detrimentally impact native southern brook trout (Salvelinus fontinalis) in Great Smoky Mountains National Park (GRSM) headwater streams. To test the hypothesis that episodes of stream acidification cause physiological distress to native trout, caged fish at three sites were exposed to acid episodes during in situ bioassays conducted in June 2006 and March 2007. Stream pH decreased (>0.7 pH units) and total dissolved aluminum (Al(TD)) increased (>175 microg/L) at all three sites during acid episodes in both bioassays. Whole-body sodium concentrations were significantly reduced (10-20%) following the acid episodes, when preceding 24-h mean pH values of 4.88, 5.09, and 4.87 and corresponding 24-h time-weighted average Al(TD) concentrations of 210, 202, and 202 microg/L were observed. Lower whole-body sodium concentrations were correlated with elevated H+ and Al(TD) concentrations. Loss of sodium ions in native southern brook trout was consistent with physiological distress resulting from acid exposure reported in salmonids in other investigations. Further research is necessary to conclude whether acid episodes are responsible for extirpation of brook trout from headwater streams in the GRSM.