Phytoplankton assemblages are of great importance as indicators of water quality. However, knowledge of New Jersey freshwater phytoplankton assemblages is very limited. We collected a total of 196 samples between June and October each year from 2016 to 2019 and analyzed them for water-quality parameters, microcystins, and phytoplankton community composition. We documented a total of 91 phytoplankton taxa. The cyanophytes were the most dominant phytoplankton group statewide and by ecoregion, with Synechococcus being the most frequently observed cyanophyte. Fluorescence of phycocyanin significantly correlated with cyanobacterial cell density and microcystins, suggesting phycocyanin can be used as a proxy for estimating harmful cyanobacterial blooms (HCB) conditions. The results of this study provide insight into the freshwater phytoplankton communities during the HCB season and their relationship with water-quality conditions in New Jersey.