The influence of trophic status on the distribution of hydrophobic organic contaminants (HOCs) in different subtropical shallow waters at large spatial scales remains largely unknown. In this study, samples of surface sediments, water, total suspended particles, phytoplankton, and zooplankton were simultaneously collected from 83 sampling sites in 20 subtropical oligotrophic to hyper-eutrophic shallow lakes in China to investigate the influence of trophic status on the spatial distribution and sinking fluxes of 16 polycyclic aromatic hydrocarbons (PAHs). The total concentration of the 16 PAHs (ΣPAH16) in the water columns of these lakes varied from 0.22 to 5.81 μg L-1, and increased with the trophic state index (TSI) and phytoplankton biomass. Phytoplankton were the dominant reservoir for the PAHs in the water column. However, the fraction of ΣPAH16 in phytoplankton decreased with the TSI. The average sinking flux of ΣPAH16 of the individual lakes varied from 2257.1 to 261674.1 mg m-2 d-1, and increased with the TSI of the lakes. The concentration of ΣPAH16 in the surface sediments ranged from 385.77 to 3784.37 ng gdw-1, and increased with the TSI and the ratio of phycocyanin/sediment organic carbon. It suggested that cyanobacterial biomass affected by trophic status dominated the occurrence of the PAHs in the surface sediments of these lakes. Biomass dilution and the biological pump affected the accumulation of the PAHs in phytoplankton, and zooplankton, and had more influence on the PAHs with higher hydrophobicity. Both the bioconcentration factors and bioaccumulation factors of the PAHs decreased with the TSI. No biomagnification was observed for the PAHs from phytoplankton to zooplankton in these lakes in spring. Our study provided novel knowledge for the coupling between eutrophication and HOCs in 20 subtropical shallow lakes with different trophic status.