The pollution characteristics, spatiotemporal variation, sediment–water partitioning, and potential ecological risk assessment of phthalate esters (PAEs) in the sediment–seawater system of the Hangzhou Bay (HZB) in summer and autumn were researched. The sum of the concentrations of the 10 PAEs in seawater ranges from 7305 ng/L to 22,861 ng/L in summer and from 8100 ng/L to 33,329 ng/L in autumn, with mean values of 15,567 ± 4390 and 17,884 ± 6850 ng/L, respectively. The Σ16PAEs in the sediments are between 118 and 5888 μg/kg and 145 and 4746 μg/kg in summer and autumn, respectively. The level of PAEs in seawater varies with the seasons, but it is relatively stable in the sediments. Di(2-ethylhexyl) phthalate (DEHP), di-n-butyl phthalate (DnBP), and diisobutyl phthalate (DiBP) are the predominant PAE congeners in the HZB. The DnBP and DiBP concentrations in seawater are greater than the DEHP concentration, which is the opposite in the sediments. The sediment–seawater equilibrium distribution study indicates that the PAEs with medium molecular weights, such as DiBP, butyl benzyl phthalate, and DnBP, are near dynamic equilibrium in the sediment–seawater system; PAEs with high molecular weights (e.g., di-n-octyl phthalate and DEHP) tend to transfer from water to the sediments; and PAEs with low molecular weights (e.g., dimethyl phthalate, diethyl phthalate, and diamyl phthalate) tend to spread to seawater. The risk assessment results in seawater indicate that DEHP and DiBP might pose high potential risks to sensitive organisms, and DnBP might exhibit medium ecological risks. In the sediment, DiBP might display a high potential risk to fish, and the potential risk of DEHP is high in several sites.