Spatial distributions and partitioning of polychlorinated biphenyls (PCBs) in Tokyo Bay, Japan, were evaluated by measuring the concentrations of all 209 PCB congeners in surface and bottom waters and bottom sediment at 10 locations. The dissolved + particulate summed congener concentrations (ΣPCB [sum of the concentrations of all 209 PCB congeners]) in surface and bottom waters ranged from 120 to 1100 pg L⁻¹ (median 250 pg L⁻¹) and from 83 to 910 pg L⁻¹ (median 230 pg L⁻¹), respectively. The concentrations did not statistically differ between the two layers, possibly because of vertical mixing of the water column. ΣPCB concentrations in sediment ranged from 2.7 to 110 ng g⁻¹-dry weight. The highest ΣPCB concentrations in both water and sediment were found at stations in the northern bay. Logarithms of field-observed organic carbon-normalized partition coefficients (K_OC) increased linearly as the log octanol–water partition coefficients (K_OW) increased, up to a log K_OW of about 6.5, and then decreased for log K_OW > 6.5 (mostly hexa- and hepta-chlorinated biphenyls). Furthermore, log K_OC values of congeners having log K_OW < 6.5 were higher by about 1 than values predicted by a published empirically derived equation, suggesting that application of K_OC values determined in laboratory experiments with soil or sediment samples to fate prediction models may result in overestimation by about one order of magnitude of the concentrations of PCBs with log K_OW < 6.5 in the dissolved phase in the water column.