This U.S. Geological Survey (USGS) Data Release provides phytoplankton data collected from Milford Lake and the Republican River, Kansas, during May 2016 through June 2020. All data are reported as raw calculated values and are not rounded to USGS significant figures. This data release was produced in compliance with the federal open-data requirements as a way to make scientific products associated with USGS research efforts and publications available to the public. The dataset includes all routine and quality assurance/quality control samples collected at 42 USGS sample locations at Milford Lake and 1 USGS sample location on the Republican River. Phytoplankton were identified to the lowest possible taxonomic level and abundance (density) and biovolume are reported.