Polycyclic aromatic compounds (PACs), including harmful polycyclic aromatic hydrocarbons (PAHs) and more toxic derivatives, are continuously released contaminants. Their provenance and dynamics in coastal oceans remain poorly understood. This study presents the first comprehensive assessment of PACs in coastal oceans by combining their presence with key hydrological and biogeochemical indicators, and potential microbial degradation. High concentrations of Σ92PACs (48–660 ng/L) were observed in the East China Sea, influenced vertically by upwelling and related sediment resuspension during winter. Spatial heterogeneity reveals distinct distribution patterns: PAHs and alkyl-PAHs were mainly influenced by riverine inputs, horizontal transport via coastal currents, and fronts acting as barriers, in contrast, oxygen-PAHs and nitro-PAHs were primarily shaped by secondary transformations within warm water masses rich in nutrients. The relationship between dissolved PACs and chlorophyll a underscores the dominance of biodegradation over the marginal biological pump effect during wintertime low primary productivity. Metagenomic analysis further highlights microbial degradation as a crucial PAC removal pathway, with enhanced microbial diversity driven by terrigenous advection and upwelling. The methodologies and findings of this research provide valuable insights into PAC cycling in coastal oceans.