The presence of polycyclic aromatic hydrocarbons in the environment has caused global concerns due to their adverse effects on living organisms. Photocatalysts have emerged as a suitable solution for this problem. The present study introduces an innovative approach in which a magnetic ternary heterojunction photocatalyst based on spinel zinc ferrite (ZnFe2O4), tri-cobalt tetraoxide (Co3O4), and bentonite was synthesized. The photocatalytic degradation of naphthalene was carried out by ZnFe2O4-bentonite-Co3O4 under solar irradiation. The effects of six operating conditions including photolysis, adsorption, type of catalyst, dosage of photocatalyst, initial naphthalene concentration, and initial pH value were checked experimentally. Under optimized conditions, the ZnFe2O4-bentonite-Co3O4 heterojunction photocatalyst could altogether remove naphthalene. In addition, a high potential was observed in the practical application of the ZnFe2O4-bentonite-Co3O4 system for the degradation of naphthalene in tap water, seawater, wastewater and soil contaminated with naphthalene. The impact of irrigation on the growth of wheat plants was evaluated. It was proved that the ZnFe2O4-bentonite-Co3O4 system could degrade naphthalene into non-toxic intermediates, and the seed germination rate was even higher using treated water compared to distilled water. Quench experiments determined that all the active species participated in the photodegradation of naphthalene over ZnFe2O4-bentonite-Co3O4, and based on the findings, the S-scheme mechanism was proposed. The reusability of ZnFe2O4-bentonite-Co3O4 magnetic photocatalyst was examined and approximately 16% decrease in naphthalene degradation efficiency was observed after three consecutive runs. Overall, this study opened a new perspective for the practical application of magnetic heterojunction photocatalysts in the degradation of persistent organic pollutants in aqueous solutions and soil.