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To ensure drinking-water safety, it is necessary to understand the factors that regulate harmful cyanobacterial blooms (HCBs) and the toxins they produce. One controlling factor might be any relationship between fungi and the cyanobacteria. To test this possibility, water samples were obtained from Harsha Lake in southwestern Ohio during the 2015, 2016, and 2017 bloom seasons, i.e., late May through September. In each water sample, the concentration of the filamentous fungus <i>Cladosporium cladosporioides</i> was determined by quantitative PCR (qPCR) assay, and <i>Microcystis aeruginosa</i> microcystin-gene transcript copy number (McyG TCN) was quantified by reverse-transcriptase qPCR (RT-qPCR) analyses. The results showed that during each bloom season, the <i>C. cladosporioides</i> concentration and McyG TCN appeared to be interrelated. Therefore, <i>C. cladosporioides</i> concentrations were statistically evaluated via regression on McyG TCN in the water samples for lag times of 1 to 7 days. The regression equation developed to model the relationship demonstrated that a change in the <i>C. cladosporioides</i> concentration resulted in an opposing change in McyG TCN over an approximately 7-day interval. Although the interaction between <i>C. cladosporioides</i> and McyG TCN was observed in each bloom season, the magnitude of each component varied yearly. To better understand this possible interaction, outdoor <i>Cladosporium</i> spore-count data for the Harsha Lake region were obtained for late May through September of each year from the South West Ohio Air Quality Agency. The average <i>Cladosporium</i> spore count in the outdoor air samples was significantly greater in 2016 than in either 2015 or 2017, and the <i>M. aeruginosa</i> McyG TCN was significantly lower in Harsha Lake water samples in 2016 compared to 2015 or 2017. These results suggest that there might be a “balanced antagonism” between <i>C. cladosporioides</i> and <i>M. aeruginosa</i> during the bloom season.