Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants that pose a critical threat to the health of aquatic ecosystems. Originating from anthropogenic sources, such as oil refineries, oil spills, industrial emissions, and natural sources, PAHs infiltrate aquatic environments where they exert concerning effects. This chapter explores the mechanisms of PAH toxicity, such as bioactivation by the cytochrome P450 system, which converts these compounds into highly reactive metabolites with carcinogenic, genotoxic, and endocrine-disrupting potential. Bioaccumulation and biomagnification amplify these impacts, particularly in higher trophic-level organisms, such as marine predators, increasing ecological risks along the food chain. The synergistic interactions between PAHs and emerging pollutants, such as microplastics and heavy metals, further intensify their toxicity, worsening environmental degradation and hindering the recovery of already overburdened ecosystems. Additionally, climate change accelerates these effects by increasing the bioavailability and biotransformation of PAHs under global warming and ocean acidification conditions. Finally, the chapter addresses mitigation strategies, emphasizing advanced technologies such as high-precision bioremediation and real-time predictive monitoring systems. Integrated with dynamic and adaptive environmental policies, these measures are essential to strengthening ecological resilience and ensuring the preservation of aquatic ecosystems. Only through a coordinated scientific and regulatory response will it be possible to face the growing chemical and environmental pressures threatening the stability of these environments, which are fundamental to global biodiversity.