Ten lakes and two rivers in Illinois were sampled in August–October 2012 to determine the concentrations and spatial distribution of cyanobacteria and associated cyanotoxins throughout the State. The reconnaissance was a collaborative effort of the U.S. Geological Survey and the Illinois Environmental Protection Agency. Sample results indicated that concentrations of both total cyanobacterial cells and microcystin were commonly at levels likely to result in adverse human health effects, according to World Health Organization guidance values. Concentrations generally decreased from August to October following precipitation events and lower temperatures.