Petrochemical Industries are potentially capable of impacts on environment due to the essence of the activities and producing waste water, pollutant emissions and hazardous wastes. This case study has considered the environmental adverse impacts of petrochemical industries on existing habitats in Mahshahr Economic Special Zone with respect to the regional significant biological diversity and ecological valuable species. When results from regional estuary sampling as well as impacts by petrochemical industries pollutants has been analyzed and studied. Then affected ecosystems have been prioritized using Analytic Hierarchy Process (AHP) method, Expert Choice software and Eigenvector technique. Studies outcomes show that, with regard to petrochemical industries pollutants, especially waste waters including heavy metals, oil and grease, Chemical Oxygen Demand (COD), Total Suspended Solids (TSS), along with criteria defined in AHP method such as ecological and protecting value, estuaries are most affected ecosystems in the region. On the other hand, types of fishes and benthic, such as Decapods, Gastropods and Tanaida have been highly affected by the petrochemical industries activities consequents. It is concluded that, heavy metals, oil and grease, deposit into the environment, are the most important pollutant sources for the regional estuaries which should be controlled.