This dataset contains geochemical, isotopic, and biomarker data derived from sediment cores collected in Siskiwit Bay, Lake Superior, Wisconsin, USA. The dataset supports the reconstruction of historical phytoplankton communities, including cyanobacterial blooms, and environmental conditions over the past ~5,400 years. Measurements include carotenoid and chlorophyll pigments (via high-performance liquid chromatography), stable carbon isotopes, total carbon and nitrogen content (via elemental analyzer isotope ratio mass spectrometry), radiocarbon and lead-210 dating, loss-on-ignition, and X-ray fluorescence elemental profiles. These data reveal historical shifts in phytoplankton dominance, sand layer deposition events, and transitions between cyanobacteria- and diatom-dominated community.