Global warming and eutrophication are the main factors driving the development of cyanobacterial dominance in aquatic ecosystems. We used a model linking water temperature, oxygen saturation, concentrations of PO43−, NO3−, NH4+, total dissolved iron (TDFe), and SO42− to cyanobacteria to test the turnover patterns of cyanobacterial dominance of non-nitrogen-fixing (chroococcal species) and nitrogen-fixing (filamentous diazotrophic) species. Statistical analysis was performed using decision trees. The dominance patterns of the two morphologically and ecologically distinct cyanobacterial species were associated with different environmental factors. However, SO42− was the most important factor that explained whether non-nitrogen-fixing or nitrogen-fixing species would dominate. Other important factors were water temperature, phosphate concentration, and oxygen saturation. The model for dominance of non-nitrogen-fixing species used SO42−, PO43−, and water temperature (upper layers), and SO42−, the ratio of PO43−/NH4+, and oxygen saturation (bottom layers). In contrast, water temperature, SO42−, and NH4+ in the upper layers and SO42−, NH4+, and water temperature in the bottom layers were used for the dominance of nitrogen-fixing species. The dominance of Aphanizomenon flos-aquae was explained by different sets of variables, indicating the presence of different strains of this species. The other cyanobacteria species showed dominance patterns that could be explained by one set of variables. As cyanobacterial blooms proliferate due to climate change, it is important to know which factors, in addition to phosphorus and nitrogen, are crucial for the mass development of the various cyanobacterial species.