Toxic cyanobacterial blooms are globally increasing with negative effects on aquatic ecosystems, water use and human health. Blooms? main driving forces are eutrophication, dam construction, urban waste, replacement of natural vegetation with croplands and climate change and variability. The relative effects of each driver have not still been properly addressed, particularly in large river basins. Here, we performed a historical analysis of cyanobacterial abundance in a large and important ecosystem of South America (Uruguay river, ca 1900 km long, 365,000 km2 basin). We evaluated the interannual relationships between cyanobacterial abundance and land use change, river flow, urban sewage, temperature and precipitation from 1963 to the present. Our results indicated an exponential increase in cyanobacterial abundance during the last two decades, congruent with an increase in phosphorus concentration. A sharp shift in the cyanobacterial abundance rate of increase after the year 2000 was identified, resulting in abundance levels above public health alert since 2010. Path analyses showed a strong positive correlation between cyanobacteria and cropland area at the entire catchment level, while precipitation, temperature and water flow effects were negligible. Present results help to identify high nutrient input agricultural practices and nutrient enrichment as the main factors driving toxic bloom formation. These practices are already exerting severe effects on both aquatic ecosystems and human health and projections suggest these trends will be intensified in the future. To avoid further water degradation and health risk for future generations, a large-scale (transboundary) change in agricultural management towards agroecological practices will be required. © 2023 John Wiley & Sons Ltd.