The construction of the Three Gorges Dam (TGD) in the Yangtze River raises great concern in ecotoxicological research since large amounts of pollutants enter the Three Gorges Reservoir (TGR) water bodies after TGD impoundment. In this work, effect-directed analysis (EDA), combining effect assessment, fractionation procedure, and target and nontarget analyses, was used to characterize aryl hydrocarbon receptor (AhR) agonists in sediments of the TGR. Priority polycyclic aromatic hydrocarbons (PAHs) containing four to five aromatic rings were found to contribute significantly to the overall observed effects in the area of Chongqing. The relatively high potency fractions in the Kaixian area were characterized by PAHs and methylated derivatives thereof and heterocyclic polycyclic aromatic compounds (PACs) such as dinaphthofurans. Benzothiazole and derivatives were identified as possible AhR agonists in the Kaixian area based on nontarget liquid chromatography-high resolution mass spectrometry (LC-HRMS). To our knowledge, this study is the first one applying the EDA approach and identifying potential AhR agonists in TGR.