The Nostocales and Chroococcales cyanobacteria can produce potent cyanotoxins and survive in deep zones of aquatic ecosystems by the formation of morphologically distinguishable resistance structures and temporarily latent colonies in sediments. The purpose of this study was to determine the presence and density of Nostocales and Chroococcales with toxic potential in the water-sediment interface. During four samplings in three locations of the drinking water reservoir Riogrande II, some physical and chemical variables and chlorophyll a concentration of different spectral groups were measured, density of cyanobacteria was established by conventional microscopy, and mcyD and mcyE genes were detected by PCR. The environmental factors correlated with the abundance of cyanobacteria in the water-sediment interface were pH, total phosphorus, and iron. The highest chlorophyll concentration was provided by Chlorophyceae, while chlorophyll from the cyanobacteria spectral group fluctuated between 0.07 and 3.6 mg/L in field samples. About 86 % of the total cells number corresponded to the Microcystis complex while the Nostocales represented just 3.35 %. It was possible to find evidence for cyanobacteria with toxic potential in the three sampling points through the detection of the mcyD and mcyE genes. The presence of these cyanobacteria is possibly related to their life cycle and the resuspension processes caused by the way river water enters the reservoir. Additionally, this is the first evidence that demonstrates the importance of the water-sediment interface as a reservoir of cyanobacteria with toxic potential, since they can recolonize the water column in ecosystems that supply drinking water.