Due to the increasing population of the world, the presence of harmful compounds, especially phthalate esters (PAEs), are one of the important problems of environmental pollution. These compounds are known as carcinogenic compounds and Endocrine-disrupting chemicals (EDCs) for humans. In this study, the occurrence of PAEs and the evaluation of its ecological risks were carried out in the Persian Gulf. Water samples were collected from two industrial sites, a rural site and an urban site. Samples were analyzed using magnetic solid phase extraction (MSPE) and gas chromatography-mass spectrometry (GC/MS) technique to measure seven PAEs including Di(2-ethylhexyl) phthalate (DEHP), butyl benzyl phthalate (BBP), diethyl phthalate (DEP), dibutyl phthalate (DBP), Dimethyl phthalate (DMP), di-n-octyl phthalate (DNOP), and Di-iso-butyl phthalate (DIBP). The BBP was not detected in any of the samples. The total concentration of six PAEs (Σ6PAEs) ranged from 7.23 to 23.7 μg/L, with a mean concentration of 13.7μg/L. The potential ecological risk of each target PAEs was evaluated by using the risk quotient (RQ) method in seawater samples, and the relative results declined in the sequence of DEHP >DIBP > DBP > DEP > DMP in examined water samples. DEHP had a high risk to algae, crustaceans and fish at all sites. While DMP and DEP showed lower risk for all mentioned trophic levels. The results of this study will be helpful for the implementation of effective control measures and remedial strategies for PAEs pollution in the Persian Gulf.