Current climate change scenarios predict that aquatic systems will experience increases in temperature, thermal stratification, water column stability and in some regions, greater precipitation. These factors have been associated with promoting cyanobacterial blooms. However, limited data exist on how cyanobacterial composition and toxin production will be affected. Using a shallow eutrophic lake, we investigated how precipitation intensity and extended droughts influenced: (i) physical and chemical conditions, (ii) cyanobacterial community succession, and (iii) toxin production by Microcystis. Moderate levels of nitrate related to intermittent high rainfall during the summer of 2013–2014, lead to the dominance of Aphanizomenon gracile and Dolichospermumcrassum (without heterocytes). Microcystis aeruginosa blooms occurred when ammonium concentrations and water temperature increased, and total nitrogen:total phosphorus ratios were low. In contrast, an extended drought (2014–2015 summer) resulted in prolonged stratification, increased dissolved reactive phosphorus, and low dissolved inorganic nitrogen concentrations. All A. gracile and D. crassum filaments contained heterocytes, M. aeruginosa density remained low, and the picocyanobacteria Aphanocapsa was abundant. A positive relationship (P < 0.001) was identified between microcystin quotas and surface water temperature. These results highlight the complex successional interplay of cyanobacteria species and demonstrated the importance of climate through its effect on nutrient concentrations, water temperature, and stratification.