This study examines the bioaccumulation of polybrominated diphenyl ethers (PBDEs), with a focus on PBDE-183 (2,2′,3,4,4′,5′,6-heptabromodiphenyl ether), in two fish species, Tilapia zillii and Synodontis clarias, inhabiting the Lekki Lagoon in Lagos, Nigeria. The primary objectives are to evaluate the extent of PBDE bioaccumulation and to assess the associated health risks linked to the consumption of these fish. Given the ecological and economic significance of Lekki Lagoon, understanding the sources and ramifications of PBDE contamination is essential. Sampling was conducted at various locations within the lagoon, specifically targeting areas with varying turbidity levels that may be influenced by anthropogenic activities. Tissue samples were collected from the intestines of both fish species and subjected to comprehensive histological and biochemical analyses to detect and quantify PBDE concentrations. Notably, T. zillii exhibited significantly higher levels of PBDE-183, quantified at 0.02 mg/g, compared to S. clarias. This differential bioaccumulation indicates species-specific susceptibilities, potentially arising from physiological and metabolic variances. The findings suggest that elevated turbidity levels in the habitat of T. zillii are primarily attributable to localized anthropogenic disturbances rather than contributions from upstream water influx. Such disturbances may encompass industrial effluents, urban runoff, and suboptimal waste management practices, all of which introduce PBDEs into the aquatic environment via various pathways, including direct discharge, stormwater drainage, and the improper disposal of PBDE-containing materials. This study emphasizes the critical necessity for enhanced industrial regulations, effective waste management strategies, and increased public awareness to mitigate PBDE contamination. The implementation of these measures is essential for preserving the ecological integrity of Lekki Lagoon and safeguarding its aquatic biodiversity. Ongoing monitoring and further research are imperative to track contamination trends, evaluate the efficacy of mitigation strategies, and elucidate the long-term health impacts on both fish populations and human consumers. The findings of this investigation underscore the importance of species-specific studies within the field of environmental toxicology, offering significant insights into the differential bioaccumulation of contaminants and their ecological ramifications. By addressing the anthropogenic sources of PBDEs, we can diminish their environmental and health consequences, thereby ensuring the sustainability of crucial aquatic ecosystems such as Lekki Lagoon.