An expansion of anthropogenic activity around Lagos lagoon, Nigeria, has raised concerns over increasing contaminants entering the lagoon’s ecosystem. The embryotoxicity, teratogenicity and genotoxicity of sediment organic extracts from four sampling zones around Lagos lagoon, Ilaje, Iddo, Atlas Cove and Apapa, as well as the dominant polycyclic aromatic hydrocarbons (PAHs) identified in water measured during the wet season (naphthalene, phenanthrene, pyrene, benzo[a]pyrene and a mixture of these), were assessed with Danio rerio embryos. Embryos were exposed to varying concentrations of toxicants from 0–72 h post-fertilization (hpf). Embryotoxicity at 72 hpf showed a dose-dependent increase in mortality upon exposure to extracts from all zones, except Atlas Cove. Similarly, higher levels of teratogenic effects, such as increased oedema, and haemorrhage and developmental abnormalities resulted from exposure to extracts from Ilaje, Iddo and Apapa zones. Treatment with single PAHs revealed that significant levels of detrimental effects were obtained only for phenanthrene. The modified comet assay revealed that the oxidative damage to DNA was generally low (<12 %) overall for all sediment extracts, but was significantly elevated with Ilaje and Iddo sediment extracts when compared with solvent controls. Oxidative damage was observed with the single PAHs, phenanthrene and benzo[a]pyrene, as well as with the PAH mixture. This study highlights that Lagos lagoon sediment extracts have teratogenic, embryotoxic and genotoxic properties, which are likely due to the high molecular weight PAHs present in the extracts, some of which are known or are suspected human carcinogens.