The Patos Lagoon is the largest lagoonal system in South America. Its waters are formed by a huge drainage basin (201,600 km2) situated in the most industrialized areas of the Southern state of Rio Grande do Sul. On its margins more than 3 million inhabitants live in several cities and towns. The lagoon waters are used for leisure, drinking, industry, fisheries, agriculture and navigation. A monitoring and sampling program was developed from February 1994 to January 1996 with emphasis on the estuarine area, aiming to evaluate the occurrence of algal blooms. In the last 15 years, several cyanobacterial (blue-green algal) blooms of theMicrocystis aeruginosa have been registered in the lagoon estuary. HighM. aeruginosa biomass (50 to 9,000 μg chla l−1) was observed in the whole region in late summer and autumn 1994, and early summer 1995. The LD50 of toxic bloom samples tested in mice varied from 22 to 250 mg dry weight kg body weight−1 while levels of toxicity (LC50) in the brine shrimp varied from 0.47 to 2.44 mg ml−1. Toxicity varied in different blooms, in the distances along the scum and with time, within the same bloom. The hepatotoxin microcystin-LR was identified in almost all samples.