The occurrence of continuously released polycyclic aromatic hydrocarbons (PAHs) in marginal seas is regulated by hydrological and biogeochemical processes; however, scarce knowledge is about their derivatives in marine environments. In this study, the dissolved and particulate PAHs and their alkylated/nitrated derivatives (A-PAHs/N-PAHs) in surface seawater of the southwestern Yellow Sea (YS) and northwestern East China Sea (ECS) during September 2022 were comprehensively discussed. Results confirm higher levels of Σ 26 PAHs (9.3−70 ng/L) and Σ 43 A-PAHs (13−76 ng/ L) than Σ 20 N-PAHs (0.80−6.6 ng/L). The spatial heterogeneity of contaminants was regulated by substantial riverine runoff and ocean currents. Lagrangian Coherent Structure analysis further revealed the existence of a transport barrier at the shelf break of the southwestern YS where contaminants hardly crossed and tended to accumulate. The relationship between dissolved compounds and chlorophyll a indicated both biodegradation and the biological pump contributed to the depletion of PAHs and A-PAHs from surface seawater while the biological pump was the major driver for N-PAHs, despite their complicated water−particle partition behavior due to variations in physicochemical properties in the presence of nitro groups. Source identification demonstrated that pyrogenic and petrogenic sources dominated the YS and ECS, respectively, while photochemical transformations appeared more active in the YS.