Sustainable Development Goal 6 underscores the global commitment to universal and equitable access to safe and affordable drinking water by 2030. Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants of major environmental concern due to their toxicity, mutagenicity, and carcinogenicity, posing risks to ecosystem integrity and human health. Despite these concerns, data on PAH contamination in community water systems within rapidly urbanizing regions of sub-Saharan Africa remain scarce. This study evaluated the occurrence, distribution, and bioaccumulation of PAHs in the Ijegun–Egba River, Lagos State, Nigeria. Physicochemical properties of water samples were determined using standard analytical methods, while PAH concentrations in water, sediments, and fish tissues were quantified by gas-chromatography with flame ionization detection. Visual and organoleptic characteristics, temperature, and pH (7.15) complied with World Health Organization guidelines; however, electrical conductivity (7,245 µS/cm) exceeded recommended limits, indicating significant anthropogenic influence. PAH concentrations were low in the water column but markedly elevated in sediments and aquatic biota, with the highest levels detected in fish gills, followed by sediments and muscle tissues. The contaminant profile was dominated by low-molecular-weight PAHs, particularly fluoranthene (~30%) and pyrene (~15%), along with naphthalene, anthracene, phenanthrene, acenaphthylene, acenaphthene, fluorene, and chrysene. This pattern reflects sediment-associated accumulation and trophic transfer, raising concerns about chronic exposure risks for communities dependent on the river for fisheries and domestic use. Oil depot operations and jetty-related activities were identified as major contamination sources. The findings highlight the need for strengthened monitoring, regulatory enforcement, and mitigation strategies to safeguard aquatic ecosystems and public health.