Cyanobacterial blooms are a worldwide environmental problem. This phenomenon is typically associated with eutrophication (nutrient enrichment) and changes in hydrology. In this study we analysed the distribution of planktonic cyanobacteria in Uruguay and their toxins (microcystin, saxitoxin and cylindrospermopsin), working with an interagency team (OSE, DINAMA, IM, University of the Republic and IIBCE). An historical data base (n = 3061 for 64 ecosystems, years 1980-2014) was generated. Differences between lotic and lentic ecosystems were found in terms of chlorophyll a and nutrient concentrations, usually indicating eutrophication. Two geo-referenced maps for the country were generated with cyanobacteria biomass indicators and the most relevant toxin (microcystin), according to risk levels suggested by the World Health Organization for recreational waters. The areas of greatest risk of exposure were the reservoirs of large rivers (Uruguay and Rio Negro) and Rio de la Plata beaches. In the second part of the study, up to 20 mg L-1of microcystin was quantified in bloom (scum) samples, as well as the presence of genes that suggest more microcystin varieties, potentially with greater toxicity. This study provides basic information about the distribution of cyanobacteria in Uruguayan freshwaters that will be useful for national monitoring programs and scientific research.