Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The bacterial, microscopic eukaryotic (including algae, fungi and protozoa), and metazoan communities in riparian groundwater were characterized by environmental DNA (eDNA) metabarcoding, and their associations with water quality parameters and PAH contamination levels were analyzed. The concentration of PAHs in the Beiluo River ranged largely from 35.32-728.59 ng/L, and the main sources were petroleum source, combustion of coal and biomass, and traffic emissions. The abundances of bacterial and microscopic eukaryotic communities were negatively associated with N and P, and metazoan abundance was negatively associated with TSS. The richness and diversity of multiple community structures were primarily related to the PAHs. The abundance of bacterial communities decreased possibly due to the occurrence of Pyrene (Pyr) and Fluorene (Flu) of coal and biomass combustion, while the decrease in the abundance of microscopic eukaryotic communities could be attributed to Fluoranthene (Fla), Anthracene (Ant) of coal combustion, and Acenaphthylene (Acy) of traffic emissions. The abundance of metazoan communities increased due to Chrysene (Chry) and Fla. The PAHs in the groundwater environment of the Beiluo River were characterized by low and medium ecological risk based on risk quotient. Low molecular weight (LMW) and medium molecular weight (MMW) PAHs presented higher ecosystem risk than the high molecular weight (HMW) PAHs. Overall, this study provides insights into the riparian communities altered by PAHs, offering reference to river ecological health management.