This dataset contains a tabular file of phytoplankton abundance and community composition analysis in samples collected from two sites in the Western Lake Erie Basin and one inland lake site in northeast Ohio. Samples were processed by the Ohio Water Microbiology Lab of the U.S. Geological Survey (USGS) and analyzed by BSA Environmental Inc. and during federal fiscal years 2016-2018. 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, "Predicting microcystin concentration action-level exceedances resulting from cyanobacterial blooms in selected lake sites in Ohio", in which site-specific multiple linear regression models were developed for eight sites in Ohio−six in the Western Lake Erie Basin and two in northeast Ohio on inland reservoirs−to quickly predict action-level exceedances for microcystin, a cyanotoxin commonly found in freshwaters, in recreational and drinking waters used by the public.