A system for treating sediments contaminated with organic contaminants, such as polychlorinated biphenyls (PCBs) and other contaminants polyaromatic hydrocarbons (PAHs) and dichlorodiphenyltrichloroethane (DDT) includes treating the sediments with ozone to react the contaminants. The system is particularly effective for remediation of PCBs. In an in-situ system for remediating sediments in underwater sediment beds that are contaminated with (PCBs) and other contaminants, the contaminated sediments are treated with ozone with an ozonator conveyed over the sediment bed to mix the sediment with the ozone. The ozone reacts with the PCBs to form more reactive and biodegradable products. The treated sediment is then redeposited upon the sediment bed.