The datasets including qPCR, water parameter and cyanotoxin measurements are for a manuscript "Occurrence of Toxigenic Benthic Cyanobacteria revealed by Quantitative PCR in seven river/stream sites situated across the United States". The cyanobacterial samples were collected from rivers/streams by 6 EPA region offices using various methods. The data can be referenced by the related states and others for estimating the risks of benthic cyanobacteria.