Cyanobacteria are organisms distributed worldwide and capable of adapting to various environmental conditions. They are known for their ability to produce toxins. The water bodies where they thrive are often sources of drinking water and are used for productive activities such as agriculture and recreation, representing risks to both the environment and human health. The objective of this study was to determine the presence of toxigenic cyanobacteria and characterize the aquatic environment they inhabit within the irrigation system of the Arequipa countryside, Peru. Three sampling campaigns were conducted in November 2021 and in May and October 2022. The campaigns included the analysis of a reservoir, a river, and 14 ponds. The physicochemical characterization of the water was performed both in situ and in the laboratory. Additionally, phytoplankton and periphyton samples were collected and qualitatively analyzed in the laboratory. The results revealed the presence of 13 cyanobacteria genera: Anabaena, Anabaenopsis, Aphanocapsa, Arthrospira, Calothrix, Chroococcus, Gloeothece, Leptolyngbya, Nostoc, Oscillatoria, Phormidium, Nodularia, and Microcystis, of which 10 are considered potentially toxigenic. The recorded environmental characteristics included temperatures ranging from 8.56°C to 22.68°C, pH values between 7.59 and 9.80, electrical conductivity from 191 µS/cm to 1953 µS/cm, dissolved oxygen levels from 1.22 mg/L to 20.50 mg/L, and turbidity between 1.3 FNU and 291 FNU. The highest chlorophyll concentration, recorded at sampling point MI6, was 682.6 µg/L. The results indicate that the environmental conditions of the water bodies within the Arequipa irrigation system are suitable for the development of cyanobacteria, with a significant percentage of these genera previously reported as toxin producers. This study contributes valuable data for the implementation of monitoring plans focused on managing the risks associated with the presence of cyanobacteria and cyanotoxins in waters used for recreation, agriculture, and livestock activities.