Description: Supporting data for Kovalenko et al. Limnology and Oceanography Methods includes data from the Great Lakes Biological Monitoring Program by US EPA. Included here are the aggregated phytoplankton microscopy data for pelagic phytoplankton in the Laurentian Great Lakes and simultaneously sampled fluoroprobe data for 2013-2022 along with metadata explaining fields and units of measurement. Water quality data are a subset of data collected by the US EPA integrated for phytoplankton analysis. This dataset includes turbidity, total phosphorus and chlorophyll a, with units included in column names. Data are aggregated at the station-season-year level. Details on sampling protocols and data treatment are available in the published Standard Operating Procedures referenced in Kovalenko et al. (2025). File Format: .csv Geographical Area Covered: Laurentian Great Lakes (Lake Superior, Huron, Michigan, Erie and Ontario), North America Temporal Coverage: 2013-2022 with biannual sampling in spring and summer, typically April and August Related Datasets: Raw fluoroprobe profile data are available from the EPA co-authors on reasonable request Discipline: Limnology, Phycology, Aquatic Ecology