The rapid growth of aquaculture in the state of São Paulo may be causing a number of environmental problems. The contribution to the eutrophication process is among the consequences of these undertakings, given that the tanks used in fish farming as well as the changes around these establishments are becoming eutrophic systems due to excessive nutrients. A frequent consequence of eutrophication in waters is the massive development of cyanobacteria. The occurrence of these blooms induces severe problems, as Microcystis aeruginosa, the most widespread distributed cyanobacteria, which can produce microcystin-LR. Toxic effects of MC have been described in liver, lungs, stomach, and intestine. Deaths in wildlife, livestock and human beings were also associated with microcystin exposition, which can occur directly by ingestion, inhalation, contact, intravenous inoculation of contaminated water (hemodialysis) or indirectly, by the consumption of animals, as fish and mollusks, the major ingestors of cyanobacteria and its toxins. Thus we need a program to control the quality of water tanks and reservoirs and also the fish breeded there, as cyanobacteria blooms have been found in various water bodies. This study focused on the determination of the cyanotoxins microcystin-LR, using techniques such as solid phase extraction and liquid chromatography for the detection and quantification of microcystin-LR in samples of cyanobacteria blooms. Tests performed with solid phase extraction showed that this procedure is not necessary for all the samples because there were cases where no difference was obtained in interfering peaks near the retention time of the analyte studied. As the parent of such samples are very complex and vary greatly, because the extracts contained too much coextrated material that interfered in the LC-UV detection, and depending on the way in which it is recommended to be assessed, case by case, the solid phase extraction needs to be promoted, because it is a process that demands a longer period of analysis and consequently an increase in costs. A liquid chromatography method was established and validated, which is deemed capable of providing reproducible and reliable data, by testing for selectivity, limit of detection and quantification, linearity, precision, accuracy and recovery, in accordance with the acceptance criteria of Resolution No. 899 of 2003 of ANVISA. The detection limit of the method was set at 0.1 µg mL -1 , and the lower limit of quantification at 0.5 µg mL -1 determined according to the signal to noise ratio proposed by the Validation Guide of Bioanalytical Methods, ANVISA. Quantification of microcystin-LR was performed using the matrix-matched method, which minimizes and/or offsets the effect of possible matrix interference or present in the sample. The analytical curve obtained y = 1.5888 + 21.849 x, with a coefficient of correlation of 0.997 shows a good linearity. Real aquaculture samples were analyzed that were detected and quantified according to the method developed.