This study investigates the effects on fish and assesses human health hazards from mercury released in two gold mining areas in Indonesia: Tatelu (North Sulawesi Province) and Galangan (Katingan District, Central Kalimatan Province). In Tatelu, 154 fish specimens of 10 freshwater species were collected, as well as five marine species from the fish market. The mean concentration of total mercury in muscles of freshwater fish from this area was 0.58+/-0.44 microg/g, with more than 45% of fish having Hg levels above the WHO guideline for human consumption of 0.5 microg/g. In Galangan, where 263 fish specimens of 25 species were collected, the total mercury in muscles averaged 0.25+/-0.69 microg/g. Excluding data from flooded open pits in sub-area P4, mean Hg levels in fish from Galangan were 2 to 4 times lower than 0.5 microg/g, while fewer than 10% of fish from Galangan exceeded WHO guidelines. The Hazard Quotient (HQ) was applied to both areas to determine the threat of MeHg exposure for communities in both areas. The HQ is a risk assessment indicator which defines the ratio of exposure level to a single substance in relation to a reference dose. Samples from Tatelu (excluding marine species) had an HQ above one, while those from Galangan resulted in values of 2.4 for the whole area and 9.9 for sub-area P4, pointing to potentially harmful fish consumption for the local population. By using the single-compartment model to estimate mercury levels in blood and hair from daily intake dose, sub-area P4 showed the highest levels, higher than the upper limit guideline for pregnant women, but still lower than threshold levels associated with observed clinical effects.