The Fengshan River system is one of the major rivers in Kaohsiung City, Taiwan. This study investigated the concentration of eight phthalate esters (PAEs) in sediments of the river and the impact of potential ecological risks during the dry and wet seasons. The potential risk assessment of sediment PAEs was evaluated by adopting the total risk quotient (TRQ) method. The total PAEs concentrations (∑PAEs) in the sediments of the Fengshan River system are between 490–40,190 ng/g dw, with an average of 8418 ± 11,812 ng/g dw. Diisononyl phthalate (38.1%), bis(2-ethylhexyl) phthalate (36.9%) and di-isodecyl phthalate (24.3%) accounted for more than 99.3% of ∑PAEs. The concentration of ∑PAEs in sediments at the river channel stations is higher during the wet season (616–15,281 ng/g dw) than that during the dry season (490–1535 ng/g dw). However, in the downstream and estuary stations, the wet season (3975–6768 ng/g dw) is lower than the dry season (20,216–40,190 ng/g dw). The PAEs in sediments of the Fengshan River may have low to moderate potential risks to aquatic organisms. The TQR of PAEs in sediments at the downstream and estuary (TQR = 0.13) is higher than that in the upstream (TQR = 0.04). In addition, during the wet season, rainfall transported a large amount of land-sourced PAEs to rivers, leading to increased PAEs concentration and potential ecological risks in the upper reaches of the river.