Nutrient loading has resulted in the proliferation of harmful algal blooms (HABs) in freshwaters worldwide. Most HABs are composed of cyanobacteria, also known as blue‐green algae, which can harm human and animal health when they produce cyanotoxins. Ubiquitous HABs represent a serious problem across waterbodies in New York State and the Finger Lakes. Studies of algal community dynamics can help illuminate factors that lead to increases in HABs. Advanced sensor technology allows for in situ measurements of chlorophyll differentiated by algal class. In this study, a FluoroProbe spectrofluorometer (bbe moldaenke, GmbH) was used to assess four major phytoplankton groups in the pelagic and nearshore of two Finger Lakes (i.e., Honeoye and Canandaigua Lakes). The objective of this work was to determine whether pelagic sampling reflects nearshore algal communities, and how this varies by lake trophic status. Seasonal changes in algal communities were also assessed, and water quality parameters that best explain phytoplankton succession and specifically cyanobacteria are evaluated.