Sediments from Mtoni estuary and 2 tributaries, Tanzania, were screened for polychlorinated-p-dibenzodioxins, -dibenzofurans (PCDD/Fs) and dioxin-like PCBs (dl-PCBs) using the chemically activated luciferase gene expression (CALUX) bioassay approach. PCDD/Fs expressed as bio analytical equivalence (BEQ) values ranged from 5.7 ± 1.4 to 39.9 ± 5.8 pg BEQ/g sediment in the wet season and from 14.1 ± 2.0 to 32.8 ± 4.7 pg BEQ/g sediment in the dry season, with higher levels observed in Kizinga River and stations close to the mouth of that river. Dioxin-like PCB levels ranged from 0.21 ± 0.03 to 0.53 ± 0.03 pg BEQ/g sediment in the wet season and from 0.22 ± 0.03 to 0.59 ± 0.04 pg BEQ/g sediment in the dry season. Higher PCDD/F and dl-PCB levels in sediments are probably related to open burning of plastic scraps, household burning of wood or charcoal and traffic related emissions, all of which occur in the Dar es Salaam region. The denser population and the more intense industrial activities in the Kizinga River basin may explain the enhanced PCDD/F and dl-PCB levels observed in the sediments of that river compared to the levels in the Mzinga River basin. A third sampling campaign, including also stations in the downstream estuary, confirmed the enhanced levels in the Kizinga River (maximum of 400 pg-BEQ/g) and also showed that a clear decreasing concentration gradient in the downstream direction exists. It cannot be excluded that the levels of these pollutants in the sediments of the Mtoni estuary pose a threat to the local biological community.