Harmful algal blooms are important threats to reservoir condition. Over a 15-year period, we sampled five Argentinian reservoirs to identify the responsible species for harmful algal blooms and determine the water quality factors driving their occurrence. These reservoirs exhibit diverse morphological and hydrological characteristics and are distributed across varying climatic zones. Cyanobacterial blooms included an array of species, including toxin producers such as Raphidiopsis raciborskii, Aphanizomenon gracile, and Microcystis aeruginosa. In contrast, dinoflagellate blooms were predominantly characterized by Ceratium. The cyanobacterial blooms primarily occurred in the shallower reservoirs located in warmer regions, whereas dinoflagellate blooms occurred where temperatures were lower. The most intense blooms occurred during the summer, and although cyanobacterial and chlorophyte blooms co-occurred, they never coexisted with dinoflagellate blooms. We identified cyanotoxins in the reservoirs over the past three years, a phenomenon previously unreported in the region. Given that these reservoirs are drinking water sources for human populations, ongoing and systematic monitoring is needed to protect public health. Controlling the proliferation of algae and cyanobacteria in reservoirs requires resource management at the watershed level, and in the case of the Itiyuro and El Limón, requires binational management with Bolivia.