Cyanobacteria commonly grow in the benthic periphyton of streams and rivers around the world, but they often are small contributors to biomass production. However, observations of benthic cyanobacterial blooms and toxin production have led to growing concerns in recent decades because they potentially are emerging threats to these ecosystems, animals, and human health and wellbeing. This has created a need to better describe and understand the distributions and ecology of cyanobacteria taxa in streams and rivers. The U.S. Environmental Protection Agency has morphological-based identifications, cell densities and “natural units”, and biovolume data for cyanobacteria collected during the 2008/2009 and 2013/2014 National Rivers and Streams Assessment (NRSA) and 16S rRNA gene metabarcoding data from the 2018/2019 NRSA. Here, we use these data to summarize national and regional distributions of benthic cyanobacteria taxa, including potential toxin producers, and to examine their possible relationships with environmental variables. Of particular note, DNA metabarcoding showed that Microcoleus autumnalis more frequently had greater relative abundances of gene reads and was more widely distributed (714 of 1852 samples) than other potential toxin producing taxa. This species also occurred in the greatest proportions of samples collected from sites in the Northern and Southern Appalachians and the Western Mountains and Xeric ecoregions (and Wisconsin). While this work provides the first national scale results describing the distributions of cyanobacteria taxa, DNA-based approaches are unable to provide information on their biomass, and morphology-based approaches face challenges associated with reliable identification and biomass measurements. Along with other possible measurements, such as qPCR of toxin producing genes, pigment analysis, and improved field methods and quantitative visual assessments, these approaches could collectively improve the understanding, monitoring, and management of benthic cyanobacterial blooms.