The pollution of water by heavy metals is one of the most serious problems in the developing countries, where watercourses play important roles in transport and economic activities. The aim of this study was to examine whether Hyposarcus pardalis, a fish species widespread in the freshwater environment in Indonesia could be used as a biomarker for pollution of the environment by metals. To this effect, the concentrations of metallothioneins and metals in the livers and kidneys of Hyposarcus pardalis were measured. In addition, to clarify the relationship between metallothionein concentrations and metal exposure, the concentrations of metallothioneins and metals were determined in the liver and the kidney of fish exposed to 50 and 500 ppb Cu and 500 ppb Mn, compared with those kept in clean water. Sufficient concentrations of metallothionein were detected in fish captured from Lake Rawakalong located in an industrial area in the suburbs of Jakarta. The results of exposure experiments suggested that Hyposarcus pardalis retained a history of pollution in its organs for a long duration, and the metals bound to metallothioneins in the liver and kidney could be replaced with Cu following exposure. In conclusion, the hepatic and renal metallothioneins in Hyposarcus pardalis are a useful candidate biomarker for monitoring heavy metal contamination.