Genomic characteristics like genome size and GC content provide insight into the evolution of microbes as well as the mechanisms of selection that influence the structure and function of microbial communities. Genome size and GC content can vary systematically with environmental conditions. Smaller genomes may have a selective advantage in low nutrient environments by lowering reproductive costs. Lower GC content can be indicative of low nitrogen environments because there are fewer nitrogen molecules in GC relative to AT base pairs. Genomic streamlining, reduced size and lower GC content, has been hypothesized to explain the lower genome size and GC content of microbes in marine compared to soil environments. Although marine and soil microbiomes are well studied less research has been done on inland freshwaters. To compare genomic traits in streams, soil, and marine environments, we analyzed 70 metagenomes from the National Ecological Observation Network (NEON) gathered from 21 streams across the United States to assess how genetic traits vary across selected environmental variables. We used the ‘microbecensus’ program to analyze metagenomes. The findings showed that average genome size of the streams was 5.5 Mbp, with 53% GC which are intermediate between marine and soil values. Benthic samples were dominated by bacteria (79%), followed by eukaryotes (19%) and archaea (2%) Proteobacteria was the most common phylum (54%). Genome size was negatively correlated with both carbon and nitrogen concentrations, which we suggest is related to carbon use efficiency and nutrient limitation. Both genome size and GC content were positively correlated with temperature. These relationships indicate that both water chemistry and temperature induce selective changes in stream benthic microbiome characteristics.