The spatial distribution and seasonal variation of 16 phthalate esters (PAEs) in water, suspended particulate matter (SPM) and sediment were investigated in the Jiulong River estuary, Fujian, Southeast China. Of the 16 PAE congeners analyzed, only six PAEs, including dimethyl phthalate (DMP), diethyl phthalate (DEP), diisobutyl phthalate (DIBP), di-n-butyl phthalate (DBP), di(2-ethylhexyl) phthalate (DEHP) and diisononyl phthalate (DINP), were identified and quantified. The total concentrations of the six PAEs (∑6PAEs) detected for all seasons ranged from 3.01 to 26.4μg/L in water, 1.56 to 48.7mg/kg in SPM, and 0.037 to 0.443μg/kg in sediment. DEHP, DIBP and DBP were the most abundant PAE congeners in all of the water, SPM and sediment phases. The spatial distributions of PAEs in the estuary were controlled not only by the riverine runoff, seasons, hydrodynamic condition and human activities but also the physicochemical properties of PAEs.