Legionella is a genus of environmental bacteria containing pathogenic species such as Legionella pneumophila that are responsible for potentially fatal respiratory infections including Legionnaires’ disease and Pontiac fever. Disease etiology can involve Legionella replication intracellularly with protists and this study aimed to characterize the Legionella-protist relationship with the goal of developing novel outbreak prevention strategies. Water and sediment samples were collected from a water-cooling tower in South Carolina over a 6-month period. Concomitantly, multiple environmental parameters were recorded. Bacterial and eukaryotic communities were characterized using the 16S rRNA gene V4 region and a 252 bp fragment of the 18S rRNA gene, respectively. Co-occurrence network analyses were performed to elucidate Legionella-protist correlations through time. We found that Legionella correlated with different protists as the seasons progressed. Acanthamoeba correlated with Legionella in early spring followed by Vannella and Korotnevella in late spring and early summer, joined by Echinamoeba in mid-summer. Vannella and Acanthamoeba are known potential hosts for Legionella, while Korotnevella is a potential undocumented host. Of the environmental parameters, temperature showed a strong correlation with protist species, suggesting that Legionella frequency was driven by temperature-dependent protist availability. Understanding which protists aid Legionella persistence in water systems will advance our knowledge of the pathology of Legionnaire’s disease and provide potential targets to help predict and prevent disease outbreaks.