Palu bay waters is susceptible to heavy metal pollution due to the inclusion of the waste product of Palu city, and such as agriculture, and traditional mining. The objective of this research was to determine the contamination of heavy metals mercury (Hg) and lead (Pb) in water, sediment, and torpedo scad fish (Megalaspis cordyla) Sampling was done purposively at 10 sampling points. Parameters of water quality measurements were done in the field for temperature, pH, brightness, turbidity, and dissolved oxygen (DO), and at laboratory analysis for salinity, chemical oxygen demand (COD), ammonia, and nitrates. Heavy metals were analized by following APHA, and Indonesian National Standard (SNI) methods. The results showed that Hg consentrations in water, sediment, gill, meat, liver, and spleen were 0.0008-0.0042 mg/l, 0.017-0.287 mg/kg, 0. respectively. Pb concentrations in water, sediments, gill, meat, liver, respectively. The average of Hg and Pb concentrations in the water had exceeded the specified quality standards, while in the sediment were still below the quality standards. The average of Hg and Pb concentrations in all observed fish organs were below the quality standards, except for Pb concentrations in gill, liver, and spleen.