Heavy metal contamination comes from the air, soil, and water, which affect the animals, plants, and humans in the food chain loop. Duck meat is one of the protein sources for humans and can be used as an indicator of heavy metal pollution. In this research, cross-sectional analytic research was carried out to analyze heavy metal contamination in duck meat. The water, feed, and duck meat (thigh and chest) samples from in intensive duck farming in Central Java, Indonesia, were taken randomly. The metal contents were measured and analyzed using Inductively Coupled Plasma (ICP-OES), followed by the manufacturer’s procedure. Six tolerable heavy metals (Ag, Al, Cr, Cu, Ni, Sr) were found in water, feed, and duck meat which were still under the tolerable threshold with the highest concentration was Al and Cu, at 0.98 ± 0.025 ppm and 0.68 ± 0.117 ppm, respectively. The essential heavy metals were found in duck meat, including Fe and Zn. The dangerous heavy metal Hg contamination was found in Semarang duck meat (5.54 ± 0.01 ppm), followed by Magelang (4.84 ± 0.00 ppm) and Salatiga (4.56 ± 0.00 ppm). All water samples from five locations were contaminated with As, Hg, Cd, and Pb, which exceeded the national standard. The presence of Hg in meat is positively correlated with the concentration of Hg in water (p = 0.002) and feed (p = 0.02) and influences simultaneously (R2 = 0.788; p < 0.05). The best possibility of heavy metal contamination in duck meat is the accumulation of water and feed consumption. Therefore, there is a need for special attention from the farmers on the duck feed for achieving meat safety as an effort to maintain food security.