The Asembagus irrigation area (East Java, Indonesia) receives a high input of fluoride (F) via surface water that partially originates from the hyperacid crater lake of the Ijen volcano. Endemic dental fluorosis among local residents has been ascribed to F in water wells. In this study, the total F intake by children and adults was estimated, based on concentrations in well waters and foods throughout the area. These values were compared with the Lowest Observed Adverse Effect Level (LOAEL) for dental fluorosis among children and skeletal fluorosis among adults. Fluorosis hazard maps were prepared, identifying the most hazardous locations in the area. It was concluded that there is not only a high risk of dental fluorosis, but also of skeletal fluorosis. Based on the total daily intake, the lowest F concentration in drinking water that poses a risk of developing fluorosis is approximately 0.5 mg/l for dental fluorosis and 1.1 mg/l for skeletal fluorosis. This is below 1.5 mg/l, which is both the guideline value for drinking water from the World Health Organization (WHO) and the Indonesian drinking water standard. This is the first documented case of human health problems that may be directly associated with natural pollutants originating from a volcano-hosted crater lake.