This U.S. Geological Survey (USGS) data release contains meteorological, water temperature, light (photosynthetically active radiation and illumination), and multichannel fluorescence sensor data from the Finger Lakes Region of New York, during the fall of 2018 and the summer and fall of 2019 and 2020. It also includes all sensor data and associated discrete sample data, at the near surface (top), mid-depth (middle) and near bottom (bottom) depths. Data were collected from three Advanced Monitoring Pilot study platforms in open water at Seneca Lake (USGS station number 425027076564401), Owasco Lake (USGS station number 425327076313601), and Skaneateles Lake (USGS station number 425606076251601) in 2018 and 2019, and in Seneca Lake and Owasco Lake in 2020 The dataset includes laboratory-measured chlorophyll-a, nitrate plus nitrite, dissolved organic carbon, biovolume of cyanobacteria, biovolume of green/brown algae, biovolume of phycoerythrin-containing phytoplankton, biovolume of other phytoplankton, biovolume of total phytoplankton, and sensor-measured chlorophyll concentration from cyanobacteria, chlorophyll concentration from mixed phytoplankton, total chlorophyll concentration, chlorophyll concentration from green/brown algae, percent green/brown algae, percent cyanobacteria, percent mixed phytoplankton, dissolved organic matter relative fluorescence, fluorescent dissolved organic matter concentration, water temperature, specific conductance, dissolved oxygen, pH, chlorophyll relative fluorescence, fluorescent chlorophyll concentration, phycocyanin relative fluorescence, fluorescent phycocyanin concentration, orthophosphate, turbidity, nitrate plus nitrite, illumination, wind speed and direction, air temperature, precipitation and photosynthetically active radiation.