Headwater streams are crucial for the health and resilience of entire watersheds; therefore, understanding how human activities disrupt the structure and function of these vulnerable ecosystems is paramount. Bacterial assemblages respond to a myriad of environmental changes and have the potential to indicate subtle anthropogenic impacts to relatively pristine headwater streams. We collected benthic samples from 46 headwater streams throughout the upper Delaware River Basin, USA. Streams were relatively pristine with upstream forest cover >50%. Bacterial community compositions for each stream were characterized following DNA extraction, amplification of the 16S rRNA V4 gene, and sequencing. Nonmetric multi-dimensional scaling was used to visualize between-site differences and potential relationships with environmental variables. We found that variation in bacterial community composition was most strongly related to sodium concentration with canopy cover being secondarily important. These results suggest that road salt associated with winter road deicing and changes in algal dominance of stream biofilms associated with reduced riparian canopy can have measurable effects on the microbial assemblages.