Semivolatile organic compounds (SVOCs), typified by polycyclic aromatic hydrocarbons (PAHs), are notorious pollutants that significantly affect aquatic ecosystems and public health. Sediments serve as major sinks for anthropogenic PAHs. However, their role in modulating the risks that PAHs pose to aquatic ecosystems under climate change scenarios remains underexplored. We combined a global meta-analysis of PAH concentrations in air, water, and sediment from 1993 to 2021 with a robust multimedia fugacity model to assess PAH transport and distribution. The toxicity equivalent concentration approach was used to calculate the risk ratio and dioxin toxicity equivalent of PAHs. The majority of reported measurements clustered in three major watersheds: the Yangtze (n = 488) and Huanghe (n = 196) in China and the St. Lawrence (n = 337) in the United States. Sediment sinks contribute substantially to the persistence and redistribution of PAHs. By 2050, high-molecular-weight PAHs will dominate the sediment–water exchange pathway, whereas low-molecular-weight PAHs will be largely depleted in sediments, primarily driven by projected shifts in the composition of emissions, enhanced volatilization and degradation of low-molecular-weight compounds, and the absence of continuous external inputs. Climate-induced changes in sediment fluxes are predicted to elevate aquatic PAH concentrations and the associated risks in China, quantified by the risk quotient and dioxin toxicity equivalence. Although this trend holds for most regions, the St. Lawrence watershed is projected to experience lower ecological risk owing to higher PAH degradation rates. This research underscores the critical role of sediment sinks in shaping the risks posed by PAHs in climate change scenarios and emphasizes the need for integrated management strategies, including sediment remediation and climate change adaptation.