ObjectiveTo investigate whether exposure to Murray River and allied water sources during a period of raised cyanobacterial cell counts was associated with gastrointestinal and dermatological symptoms.DesignA case‐control study selecting gastrointestinal and der‐matological cases and controls from subjects attending 21 general practitioners in eight Murray River towns. The association between the proportion of consultations for such symptoms and mean log cyanobacterial count was also examined.Subjects102 gastrointestinal cases, 86 dermatological cases and 132 controls.Main outcome measureThe relative odds of gastrointestinal and dermatological symptoms, respectively, as opposed to no such symptoms, according to water‐contact history during the week preceding the medical consultation.ResultsAfter adjusting for con‐current risk factors, subjects drinking chlorinated river water rather than rain water had a raised risk of gastrointestinal symptoms(P=0.008), and those using untreated river water for domestic purposes rather than rain water had a raised risk of gastrointestinal (P= 0.034) and of dermatological (P= 0.048) symptoms. The proportion of consultations for gastrointestinal and dermatological symptoms correlated on a weekly basis with the mean log cyanobacterial cell count, although statistical significance was not achieved for the correlation with dermatological consultations or for separate reaches of the river.ConclusionsThe raised risks of gastrointestinal and dermatological symptoms in those using Murray River water for drinking and other domestic purposes are consistent with causal relationships. However, the evidence for adverse health effects is, at best, only suggestive. Further research is indicated.