Coastal environments near industrial activities are often contaminated by a wide range of pollutants, including those that can activate aryl-hydrocarbon receptor-mediated effects (AhR agonists) such as dioxins and polycyclic aromatic hydrocarbons (PAHs). However, despite several recent reports on the occurrence of unmonitored AhR agonists such as methyl-substituted PAHs (MePAHs) and styrene oligomers in marine sediments, comprehensive studies on AhR agonists in coastal environments are still lacking, especially for biota. This study evaluated the in vitro AhR agonist activities in 29 bivalve samples collected from industrially impacted coastal areas of Seto Inland Sea (Japan) in 2017–2019, and used effect-directed analysis for identification of major AhR agonists. AhR agonist activities in the cleaned-up bivalve extracts, evaluated using an AhR reporter gene assay (PAH-CALUX) and expressed as benzo[a]pyrene-equivalent (BaP-EQ), were from 140 to 18000 ng BaP-EQ/g lipid. Common PAHs, target-analyzed using GC–qMS, could explain in average only 42% of the CALUX-measured BaP-EQ values. PAH-CALUX measurement of 96 fractions of representative bivalve extracts revealed high AhR agonist activities for fractions of PAH-related compounds rather than those of dioxins. Non-target GC×GC–ToFMS analysis revealed that the major AhR agonist fraction contained methyl-substituted derivatives of benz[a]anthracene and chrysene (MeBaAs and MeChys), and several groups of other alkyl-PAHs. CALUX testing of authentic standards showed MeBaAs and MeChys as potent AhR agonists, up to 10 time more potent than BaP. Together, common PAHs, MeBaAs and MeChys accounted for >75% of the CALUX-measured BaP-EQ levels in most bivalve extracts. Unexplained AhR agonist activities in specific bivalve samples could be partially caused by mixture effects of various agonists.