This U.S. Geological Survey (USGS) data release contains phytoplankton classification and enumeration results from near-surface samples analyzed by imaging flow cytometry and collected as part of a harmful algae bloom (HAB) monitoring study conducted in collaboration with the New York State Department of Environmental Conservation (NYSDEC). Samples were collected biweekly from monitoring platforms in Owasco and Seneca Lakes and one bloom sample site at Emerson Park Boat Launch in Owasco Lake. The platforms were deployed from June-October in 2020. This dataset includes all routine and quality assurance/quality control samples collected at the three sampling locations. Phytoplankton were identified to the lowest possible taxonomic level, and abundance (density reported as both natural units and cells) and biovolume are reported. All data are reported as raw calculated values and are not rounded to USGS significant figures. This data release was produced in compliance with open data requirements to make scientific data associated with USGS research efforts and publications available to the public.