Marine plastic pollution is a major public health issue worldwide. Marine plastics release toxic persistent organic pollutants (POPs) that cause endocrine disruption, cancers, and other adverse effects on man. However, research on these compounds in the Nigerian marine environment is limited. Using a cross-sectional design and incorporating a laboratory component, this study aimed to assess the health risks associated with marine plastic pollution in the Orimedu, Idado, and Eleko communities along the coastline of Lagos, Nigeria. Sediments and water samples were collected and analysed for concentration levels of six phthalate esters (PEs) and 23 Polychlorinated Biphenyls (PCBs) using Gas Chromatography/Mass Spectrometry (GC/MS) and Gas Chromatography-Electron Capture Detector (GC-ECD) after preparation. Health risk assessment was also computed using risk assessment models developed by the United States Environmental Protection Agency (USEPA). Results obtained were compared to the World Health Organization’s (WHO) standards for cancer risk (1.0×10− 5) and non-cancer risk (≤ 1.0). Eleko had the highest concentrations of both PEs (24.89 ± 0.01 mg/L of DIOP) and PCBs (0.06 ± 0.01 of PCB 206–2,2’,3,3’,4,4’5,5’,6-Nonachlorobiphenyl) in the water samples while in the sediment samples, Idado had the highest PE (69.00 ± 0.05 of DIOP) and Orimedu was found with the highest PCB (0.09 ± 0.03 of PCB 180– 2,2’,3,4,4’,5,5’- Heptachlorobiphenyl). Most of the PEs and PCBs were above the limits set by the WHO. As such, children and adults of the three communities, especially the Orimedu community, had a high risk for carcinogenic and non-carcinogenic diseases.