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Analysis of an 18-year dataset from seven shallow lakes in Florida provides evidence of hydrologic factors controlling dynamics of cyanobacteria blooms. Depth was the most important variable, and there was a synergistic effect with flushing. When the lakes were deep, rainfall led to water discharges and disruption of stagnant conditions that maintained blooms. Factors commonly associated with bloom formation (temperature) or suppression (high organic color, which can be a light-limiting factor) did not play a significant role. A conceptual model illustrates how blooms are regulated. First, the presence of bloom-forming species, high concentrations of nutrients, and lack of large zooplankton create a potential for blooms. Second, climate cycles influence yearly rainfall, resulting in wet years and droughts that affect lake water level and volume. This either stimulates blooms (drought, shallow) or suppresses them (wet, deep). Finally, proximal drivers such as a rain events and a flush of water suppress blooms. The results illustrate how climate variability and weather can control cyanobacteria blooms by affecting several processes long known to influence bloom formation, and provide insight into how climate change might affect occurrence of blooms in nutrient-enriched shallow lakes.