One liter water samples were recovered from all redox-zones in permanently redox-stratified Fayetteville Green Lake, NY during October 2016 and July 2017, and the end and at the peak of concurrent cyanobacteria, purple and green sulfur bacteria blooms. The water samples were size-fractionated by in-line filtration into particle-associated (greater than 2.7 micrometers) and free-living (0.2 micrometers - 2.7 micrometers) assemblages. The V4-V5 hypervariable regions of the 16S rRNA genes were amplified using the primers 515FY (GTGYCAGCMGCCGCGGTAA) and 926R (CCGYCAATTYMTTTRAGTTT). 350 base-pair paired-end read sequencing of the amplicons were sequenced by the Integrated Microbiome Resource (Dalhousie U., Halifax, Nova Scotia, Canada) using an Illumina MiSeq platform.