The pollution assessment and the evaluation of potential risks in the Atlantic Coastal Region of the Democratic Republic of the Congo are still very limited. Consequently, the present study investigates for the first time the concentrations of heavy metals and persistent organic pollutants (organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and polycyclic aromatic hydrocarbons (PAHs)) in river, estuary, andmarine sediments from this area. The results highlighted high concentrations of Cr, Zn, As, and Pb exceeding the probable effect level (PEL) on aquatic life. Zn was the most dominant element detected at a range of 180–480 mg kg−1 in marine sediment, 132–382 mg kg−1 in estuary sediment, and 121–687 mg kg−1 in river sediment. Total PCBs (Σ7 × 4.3) ranged from 1995 to 20,156 μg kg−1, 2013–12,058 μg kg−1, and 1861–36,417 μg kg−1 in marine, estuary, and river sediments, respectively. Total PCBs (Σ7 × 4.3) were above PEL for all sediments, suggesting potential adverse effects on benthic organisms. The OCP, PBDE, and PAH levels were low to moderate for all sediments. Taking into consideration, the concentrations of Zn, Pb, PCBs, and DDTs, probable environmental risks, are present.