With the human intensification of agricultural and industrial activities, large amount of reduced nitrogen enter into the biosphere, which consequently results in the development of global eutrophication and cyanobacterial blooms. However, no research had reported the effect of ammonia toxicity on the algal succession. In this study, we investigated the ammonia toxicity to 19 algal species or strains to test the hypothesis that ammonia may regulate the succession of cyanobacterial blooms and the distribution of common algal species in freshwater lakes. The bloom-forming cyanobacterium Microcystis aeruginosa PCC 7806 suffered from ammonia toxicity at high pH value and light intensity conditions. Low NH4Cl concentration (0.06 mmol L−1) resulted in the decrease of operational PSII quantum yield by 50% compared with the control exposed to 1000 μmol photons m−2 s−1 for 1 h at pH 9.0 ± 0.2, which can be reached in freshwater lakes. Furthermore, the tolerant abilities to NH3 toxicity of 18 freshwater algal species or strains were as follows: hypertrophication species > eutrophication species > mesotrophication species > oligotrophication species. The different sensitivities of NH3 toxicity in this study could well explain the distributing rule of common algal species in the freshwater lakes of different trophic states. Meanwhile, the cyanobacterial bloom (e.g. M. aeruginosa) always happened at the low concentration of ammonia in summer, and disappeared with the decrease of ammonia. This may be attributed to the toxic effect of ammonia to M. aeruginosa in spring (the average and maximum ammonia concentration were 0.08 and 0.72 mmol L−1 in 33 Chinese lakes), and the low level of NH3-N in summer and fall in the lakes might be used as preferred nitrogen nutrition by M. aeruginosa, rather than with toxicity. Therefore, ammonia could be a key factor to determine the distribution of common algal species and cyanobacterial bloom in the freshwater systems.