The degradation of freshwater systems by salt pollution is a threat to global freshwater resources. Salinization is commonly identified by increased specific conductance (conductivity), a proxy for salt concentrations. However, conductivity fails to account for the diversity of salts entering freshwaters and the potential implications this has on microbial communities and functions. We tested 4 types of salt pollution—MgCl2, MgSO4, NaCl, and Na2SO4—on bacterial taxonomic and functional α‐, β‐diversity of communities originating from streams in two distinct localities (Nebraska [NE] and Ohio [OH], USA). Community responses depended on the site of origin, with NE and OH exhibiting more pronounced decreases in community diversity in response to Na2SO4 and MgCl2 than other salt amendments. A closer examination of taxonomic and functional diversity metrics suggests that core features of communities are more resistant to induced salt stress and that marginal features at both a population and functional level are more likely to exhibit significant structural shifts based on salt specificity. The lack of uniformity in community response highlights the need to consider the compositional complexities of salinization to accurately identify the ecological consequences of instances of salt pollution.