The Citarum River estuary is directly connected to the Java Sea and is characterized by high salinity and turbidity. Estuaries are heavy metal receptors from anthropogenic sources. There is the potential for heavy metals in the sediment to be released back into the water column which can cause secondary contamination in the water column, this is influenced by hydrodynamic conditions and environmental factors. Water samples at 3 depth layers (surface, middle and bottom layer or) and samples from the sediment surface were collected to study this. Heavy metals contained in water and sediment samples were analyzed by Flame AAS variant 240FS. The results of investigation showed that Co and Ni in the water column still comply the river water quality standards, Cr are included in the slightly polluted category. In the sediment, Co is categorized as moderately polluted and Cr and Ni are categorized as unpolluted to lightly polluted. Heavy metal pollution in sediments comes from heavy metals in the water column which undergo adsorption and deposition processes or vice versa. Co, Cr and Ni in the waters of the Citarum River estuary tend to be particulates that are deposited to the bottom of the estuary waters and accumulate in sediments, while only a small part of heavy metals is dissolved in the water column. The distribution of heavy metals in the water column to the sediment and vice versa tends to occur in one layer (monolayer) and describes the process chemisorption. Ni, Co and Cr have a slightly mobile level and have hydrophobic or lipophilic properties There were significant differences between the concentrations of heavy metals, especially Co and Ni (p < 0.05) in several depth layers. Co and Ni in water and sediment were significantly positively correlated (p < 0.01) which indicated that the two metals had the same fate or behavior and came from the same source.