This dataset contains a tabular file of phytoplankton abundance and community composition analysis in samples collected from eight sites in the Western Lake Erie Basin; four sites in Grand Traverse Bay, Lake Michigan; and five sites in Saginaw Bay, Lake Huron. Samples were collected and processed by the Great Lakes Science Center of the U.S. Geological Survey (USGS) and analyzed by BSA Environmental Inc. Lake Erie sample collection spanned years 2014-2018 with some sites sampled throughout this period and other sites sampled in only some years. Sample collection in Grand Traverse Bay, Lake Michigan and Saginaw Bay, Lake Huron occurred in 2015. Sample collection was focused in summer and early fall months and data only represent the community present in these seasons. Site in each basin to represent a gradient of nutrient availability for that basin and are not randomly distributed. The dataset includes phytoplankton taxa (genus and species), division, tally (number of cells counted for each taxa present), density (cells per liter), and total biovolume (cubic micrometers per liter) for each sample collected. These data can be used to assess the community composition of phytoplankton at the sites, identify cyanobacteria species, and determine abundance and biovolume of any known toxin-producing cyanobacteria. The data were part of a larger study and associated water quality and cyanotoxin data are available through the USGS National Water Information System (NWIS) by searching for site numbers.