Eutrophication is one of the most widespread problems of inland waters in the world. In many countries from North to South America, eutrophication is due to several impacts resulting from the inefficient or nonexistent wastewater treatment; the agricultural expansion with inadequate soil uses and application of chemical fertilizers; the urbanization of watersheds, the increase of intensive husbandry of cattle, pigs, and chicken; the increase of aquaculture; the construction of reservoirs; and the destruction of natural ecosystems. Basically, the increase in the internal load of nitrogen and phosphorus in lakes and reservoirs produces an increase in the biological productivity of the water bodies. As consequence, phytoplankton community in freshwater systems is mainly dominated by cyanobacteria. Despite differences in continental climate regimes, this seems to be a regular pattern along the Americas, where there are various practices related to the use of lower and upper taxonomic groups of phytoplankton for the indication of the trophic level and water quality status of freshwater systems. As was reported in numerous studies in the Americas, increase in nutrient concentrations mainly due to rich in phosphorus cause larger phytoplankton biomass and predominance of cyanobacteria such as genera Microcystis, Anabaena, Planktothrix, Oscillatoria, and Cylindrospermopsis than ever before.