The aim of this study was to investigate effects on health of exposure to cyanobacteria as a result of recreational water activities. Participants, who were aged six years and over, were interviewed at water recreation sites in South Australia, New South Wales and Victoria on selected Sundays during January and February 1995. Telephone follow-up was conducted two and seven days later to record any subsequent diarrhoea, vomiting, flu-like symptoms, skin rashes, mouth ulcers, fevers and eye or ear irritations. On the Sundays of interview, water samples from the sites were collected for cyanobacterial cell counts and toxin analysis. There were 852 participants, of whom 75 did not have water contact on the day of interview and were considered unexposed. The 777 who had water contact were considered exposed. No significant differences in overall symptoms were found between the unexposed and exposed after two days. At seven days, there was a significant trend to increasing symptom occurrence with duration of exposure (P = 0.03). There was a significant trend to increasing symptom occurrence with increase in cell count (P = 0.04). Participants exposed to more than 5000 cells per mL for more than one hour had a significantly higher symptom occurrence rate than the unexposed. Symptoms were not correlated with the presence of hepatotoxins. These results suggest symptom occurrence was associated with duration of contact with water containing cyanobacteria, and with cyanobacterial cell density. The findings suggest that the current safety threshold for exposure of 20,000 cells per mL may be too high.