The Uruguay River is the second most important river in the Río de la Plata Basin. Taxonomical composition, abundance and distribution of cyanobacteria collected at nine sampling stations in the Lower Uruguay River (Uruguay) were analyzed seasonally from 2006 to 2009. A total of 24 taxa were identified, including 13 Chroococcales, 4 Oscillatoriales and 7 Nostocales species. The genera Dolichospermum and Microcystis presented the highest number of species among the planktic water bloom–forming cyanobacteria. The highest densities of cyanobacteria were recorded in summer during a bloom, with 6.2×106 cells.ml–1, and the most abundant species were Microcystis aeruginosa and Dolichospermum cf. pseudocompactum. In this case, the toxicity analyses by HPLC did not indicate the presence of microcystin–LR. Phytoplankton growth in the Uruguay River was found not to be nutrient–limited. The high correlation of cyanobacteria densities with nitrogen and phosphorous compounds is directly related to changes in flow. Cyanobacteria densities increased with summer high temperatures in low flow conditions. The ANOSIM analysis showed no significant differences between zones and sampling sites, but there were temporal significant differences in relation to seasonal samplings. Radiocystis fernandoi Komárek et Komarková–Legnerová was recorded for the first time in Uruguay and Dolichospermum cf. pseudocompactum (Watanabe) Wackl in et al. was recorded for the first time in South America.