This research supports development of aquatic resource management strategies to address acid deposition in the Great Smoky Mountain National Park (GRSM) by 1) developing relationships between baseflow and stormflow chemical constituents and examining effects of elevation, area, geology, soil, and vegetation on stream chemistry; 2) evaluating physiological condition in brook trout in relation to changes in stream chemistry during stream acidification episodes, and 3) evaluating brook trout metrics with respect to stream chemistry, basin characteristics, and ecologically relevant hydrologic parameters. (1) Stream chemistry was monitored in eight GRSM streams considering basin area, site elevation, Anakeesta geology, soil, and vegetation. Following precipitation events, pH was significantly reduced and aluminum concentrations increased, while the concentration response of ANC, nitrate, sulfate, and base cations varied. Higher pH and ANC concentrations were observed in large and low-elevation streams. (2) Caged brook trout were exposed to two acid episodes during in situ bioassays conducted in three GRSM streams. Stream pH decreased (>0.7 pH units) and total dissolved aluminum increased (>0.175 mg/L) at all three sites during acid episodes. Whole-body sodium concentrations were significantly reduced (10-20%) when preceding 24-h time weighted average pH values (4.88, 5.09, 4.87) and corresponding 24-h aluminum concentrations (210, 202, 202 µg/L). Lower whole-body sodium concentrations were correlated with elevated proton and aluminum concentrations indicating physiological distress. (3) Water chemistry, hydrology and physical basin factors influenced brook trout distributions and densities in 16 collocated fish and water quality sampling sites (1990-2009). Higher concentrations of ANC, pH, sodium, and soil cation exchange capacity, and higher fall flows were associated with the presence of brook trout. Trout densities were higher in streams with higher concentrations of sodium, suggesting that sodium may ameliorate the effects of acid toxicity. These relationships provide useful information where GRSM managers can prioritize conservation and restoration efforts.