Algal blooms refer to the massive development of photosynthetic microorganisms in aquatic environments. Microalgae are an important source of food for the primary consumers of these ecosystems, purify water, capture atmospheric CO2 and from them a large number of products for industrial use are obtained; however, in Mexico its study is still incipient, especially with regard to blooms of freshwater species. This paper presents the results obtained from the most abundant and important algal blooms of the Ejidos de Xochimilco and San Gregorio Atlapulco Protected Natural Area. 12 samplings were carried out between the years 2012 to 2022. The samples were collected with 54 μm mesh aperture trawl and van Dorn bottle and were fixed with 4% final formalin and 1% lugol, respectively. 17 algal blooms were recorded, among the Cyanoprokaryotes are: Anabaenopsis circularis, Limnospira maxima, Microcystis aeruginosa, Planktothrix agardhii; among the Chlorophytes Monoraphidium convolutum, Ankistrodesmus falcatus, Closterium acutum, Lemmermannia tetrapedia; among the Euglenophytes Euglena viridis y Phacus pleuronectes and between the Diatoms Cocconeis placentula var. placentula, Stephanocyclus meneghinianus, Epithemia turgida var. turgida, Gomphonema olivaceum, Gomphonema parvulum var. capitata, Hantzschia amphioxys y Craticula cuspidata. Of these species, Limnospira maxima has very high nutritional value, Anabaenopsis circularis, Microcystis aeruginosa y Planktothrix agardhii are potentially toxic or carcinogenic. It should be noted that all the registered species presented great spatiotemporal variations, for the above and given their great importance, it is necessary to expand their knowledge and carry out constant monitoring, as a tool for their understanding, use and management.