Purpose <p>Polycyclic aromatic hydrocarbons (PAHs) had been detected in most soils of water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR), but there were few investigations on the distinct shifts of the PAHs degradation and microbial communities in these soils under different water level conditions. This study aims to investigate the effect of water level fluctuation on the PAHs degradation and microbial communities.</p> Material and methods <p>Soil samples were collected from different altitudes and depths in the WLFZ of the TGR at the end of the flooding period and drying period respectively. The content of PAHs (∑₁₆PAHs) were determined using gas chromatography-mass spectrometer. The feature of PAHs degradation and nitrogen cycling using enzyme-linked immunosorbent assay and polymerase chain reaction method. The shifts of microbial communities were characterized by sequencing the bacterial 16S rRNA and fungal ITS rRNA gene. The analysis of linear discriminant, molecular ecological network and correlation were used to evaluate the details of PAHs degradation, nitrogen cycling and microbes.</p> Results <p>The ∑₁₆PAHs in the WLFZ soil were higher in flooding conditions, and that of tributary stream were higher than main stream. The genes of PAHs degradation were stimulated in drying conditions. The PAHs was closely positively correlated with nitrogen cycling process in the flooding period. Both bacteria and fungi contribute to the degradation of PAHs. The biomarkers were more abundant in drying conditions, and the interaction between microorganisms during the flooding period were stronger than those during the drying period.</p> Conclusion <p>This study has demonstrated the distinct differences of the PAHs degradation and microbes in the WLFZ soil under different water level conditions. The results are of interest to understand the characteristics to PAHs distribution and degradation in the WLFZ soil of TGR in Yangtze River, China.</p>