Bacterial diversity was examined in six lakes located in the Adirondack Mountains of upstate New York. This region receives significant anthropogenic atmospheric inputs of strong mineral acids resulting in decreases in pH and acid neutralizing capacity (ANC) in many of the lakes. Statistical methods including correlation and cluster analysis were used to determine if there were significant associations between phylotypes and water chemistry variables. Direct effects of acidification, pH and ANC, were not significantly correlated with any of the broadest level taxonomic classifications (equivalent to class or order), but may be correlated with subgroups within these classifications. Indirect influences of acidification were suggested by significant correlations of phylotypes with aluminum chemistry. There were positive correlations between the relative abundance of the γ subdivision of the Proteobacteria and total aluminum (r2= 0.70, p= 0.04), monomeric aluminum (r2= 0.78, p= 0.02) and non-labile aluminum (r2= 0.92, p= 0.002). The ACK1 clade of the β-Proteobacteria (Adirondack clade 1) was correlated with monomeric aluminum (r2= 0.71, p=0.03) and non-labile aluminum (r2= 0.73, p= 0.03). Significant negative correlations were found between the relative abundance of the Cytophaga-Flexibacter-Bacteroides phylum and total aluminum (r2= 0.74, p= 0.03), and the High G+C subdivision of the Gram Positive phylum with total aluminum (r2= 0.70, p= 0.04). Dissolved organic carbon (DOC) concentrations may also influence bacteria through amelioration of aluminum toxicity and as a carbon source. There were significant positive correlations between DOC and the relative abundance of the γ (r2= 0.66, p= 0.05) and β (r2= 0.78, p= 0.02) subdivisions and the ACK1 clade (r2= 0.84, p= 0.01). Additional significant correlations were also noted between specific phylotypes and certain macro- and micro-nutrients. The results of this study indicate that water chemistry can have a direct influence on bacterial lake assemblages and that in acid stressed lakes aluminum chemistry and DOC concentrations may play a particularly important role.