Southern Appalachian high elevation watersheds have deep rocky soils with high organic matter content, different vegetation communities, and receive greater inputs of acidic deposition compared to low elevation sites within the region. Since the implementation of the Clean Air Act Amendment in the 1990s, concentrations of acidic anions in rainfall have declined. However, some high elevation streams continue to show signs of chronic to episodic acidity, where acid neutralizing capacity (ANC) ranges from 0 to 20μeqL−1. We studied three 3rd order watersheds (North River in Cherokee National Forest, Santeetlah Creek in Nantahala National Forest, and North Fork of the French Broad in Pisgah National Forest) and selected four to six 1st order catchments within each watershed to represent a gradient in elevation (849–1526m) and a range in acidic stream ANC values (11–50μeqL−1). Our objectives were to (1) identify biotic, physical and chemical catchment parameters that could be used as indices of stream ANC, pH and Ca:Al molar ratios and (2) estimate the lime required to restore catchments from the effects of excess acidity and increase base cation availability. We quantified each catchment’s biotic, physical, and chemical characteristics and collected stream, O-horizon, and mineral soil samples for chemical analysis seasonally for one year. Using repeated measures analysis, we examined variability in stream chemistry and catchment characteristics; we used a nested split-plot design to identify catchment characteristics that were correlated with stream chemistry. Watersheds differed significantly and the catchments sampled provided a wide range of stream chemical, biotic, physical and chemical characteristics. Variability in stream ANC, pH, and Ca:Al molar ratio were significantly correlated with catchment vegetation characteristics (basal area, tree height, and tree diameter) as well as O-horizon nitrogen and aluminum concentrations. Total soil carbon and calcium (an indicator of parent material), were significant covariates for stream ANC, pH and Ca:Al molar ratios. Lime requirement estimates did not differ among watersheds but this data will help select catchments for future restoration and lime application studies. Not surprisingly, this work found many vegetation and chemical characteristics that were useful indicators of stream acidity. However, some expected relationships such as concentrations of mineral soil extractable Ca and SO4 were not significant. This suggests that an extensive test of these indicators across the southern Appalachians will be required to identify high elevation forested catchments that would benefit from restoration activities.