This dataset includes benthic algae community composition data in the Colorado River near Cameo, Colorado, U.S. Geological Survey (USGS) site number 09095500, from 2022 to 2023, and from three sites in the upper White River Basin, Colorado, in 2022. Taxonomic classification of algae species is not known well in theses rivers, and this study was conducted to record different algae species present in each river system. Benthic algae were typically identified as genus or species, and biomass and biovolume were provided for taxa. The U.S. Geological Survey completed data collection in upper White River Basin in cooperation with the White River Conservation District, and the Colorado River data collection was funded by the U.S. Geological Survey Water Mission Area as part of the Next Generation Water Observing System Upper Colorado River project.