Our project evaluates the effects of sediment resuspension and Microcystis sediment populations on Harmful Algal Blooms (HABs) in Lake Erie. Within these HABs, Microcystis is a prominent species of cyanobacteria that is capable of producing the harmful hepatotoxin microcystin. The annual occurrence of HABs can lead to negative human health effects, harm wildlife, and disrupt access to drinking water supplies. As a result, the ability to accurately predict, forecast, and characterize these blooms is extremely important. Despite previous research, there has been a knowledge gap regarding the magnitude in which resuspension impacts blooms and whether there is a significant presence of sediment population of Microcystis present. The differences between Microcystis populations in the water column and sediment have also not been understood. Through the use of hydrodynamic modeling, sediment core collection, laboratory experiments, omics-based methods, and statistical modeling, we have assessed sediment resuspension’s impact on HABs. Our first objective consisted of hydrodynamic modeling to identify the strength and frequency of bottom shear stress. The second objective utilized laboratory experiments with sediment cores to measure bottom shear stress for resuspension of Microcystis. Samples taken during the sediment core experiments were processed in objective 3 using genomics to determine whether Microcystis genotypes in the blooms are the same as those found on sediments. Finally, our forth objective combined hind-casts and field observations to examine resuspension and phenology. We expect that our results will be able to improve current models, contribute information to public databases, and provide a basis for future research.