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Cyanobacterial harmful algal blooms (cHABs) pose significant ecological and public health concerns in freshwater ecosystems. Viruses, specifically phages (viruses that infect bacteria), are increasingly recognized as influential players in microbial community dynamics, yet their roles within cHABs remain poorly understood. This dissertation explores the intricate interactions between phages and their microbial hosts within the context of cHABs, revealing their potential impacts on bloom dynamics and genetic diversity. Chapter 2 delves into the temporal dynamics of phages infecting bloom-forming Microcystis aeruginosa populations in Lake Erie, a region susceptible to recurrent cHABs. Through extensive genomic analyses and a novel machine-learning model, we unveil the complex web of viral interactions within cHABs, highlighting the potential for cross-species exchange of genetic material and potential phage-driven alterations in key metabolic pathways crucial for Microcystis persistence in cHABs. Chapter 3 further explores the role of phages in cHABs more broadly by unraveling the viral community structure and its relationship with the bacterial host community beyond Microcystis. Using metagenomic data, we identify and characterize thousands of viral operational taxonomic units (vOTUs), decipher their metabolic functions, and predict their bacterial hosts. This chapter underscores the dynamic nature of viral communities within cHABs and emphasizes the impact of spatiotemporal variation on viruses and how community turnover affects virus-host interactions. Chapter 4 shifts focus to how Microcystis host evolutionary distance affects their infection profiles, by using a collection of Lake Erie Microcystis multispecies enrichments. We reveal a significant association between Microcystis strain phylogenetic relatedness and infection profiles, suggesting that hosts with similar phylogenies share comparable infection profiles. Furthermore, evidence of infection dynamics within the multispecies colonies formed by Microcystis and its associated bacteria assemblage emerges, as multiple phages are predicted to infect both Microcystis and non-Microcystis hosts within a culture. Collectively, this dissertation advances our understanding of the intricate interplay between phages and their bacterial hosts within cHABs. As such, it provides valuable insights into viral ecology as it pertains to cHABs, paving the way for future research to bolster our understanding of viruses in the wild.