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Harmful algal blooms (HAB) are ubiquitous ecological and public health hazards because they are composed of potentially toxic freshwater microorganisms called cyanobacteria. The abiotic drivers for toxic HAB are investigated using a research station deployed in a eutrophic lake in Minnesota in 2016. This research station provides full-depth water quality (hourly) and meteorological conditions monitoring (5min) at the sampling site. Water quality monitoring provides chemical, physical, and biological measurements, that is, phycocyanin concentration, a photosynthetic pigment distinct to cyanobacteria. The high cyanobacteria biovolume (BV) in the epilimnion observed in mid-July persisted until late September when it was distributed uniformly throughout the water column. A scaling relationship was developed among BV heterogeneity, thermal stratification stability, and surface water temperature. This relationship was verified in a dimictic lake the following year. The proposed scaling relationship is relevant to sampling protocols of HAB as it informs if the sample depth is representative of the entire water column. During the strongly stratified period, BV accumulated above the thermocline and in the photic zone, with distinct peaks forming occasionally both near the water surface and at locations with photosynthetically active radiation approximately equal to 10 E/m(2)s. Our observations suggest that the temporal/vertical variability of cyanobacteria BV is strongly influenced by lake dynamics, thermal structure, seasonal temperature variation, and light availability. These observations demonstrate that cyanobacteria tend to move and accumulate in specific warm water layers, confined by the thermocline and determined by well-defined light conditions.