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Phthalates (PAEs) and alkylphenols (APs), known as endocrine-disrupting compounds (EDCs), are ubiquitous in aquatic environments worldwide and may be harmful to aquatic ecosystems. This study is the first to comprehensively assess the occurrence and potential ecological risks of 12 EDCs in the surface sediments of seven major harbors in Taiwan. In addition, a correlation model was established between the concentration levels of individual PAEs and APs in the sediments and their production. The total PAEs concentrations in the sediments ranged between 129–1894 ng/g dw (mean: 558 ± 479 ng/g dw). Total APs concentrations ranged betweenr = 0.989, p < .01), reflecting the status and degree of anthropogenic pollution. The concentrations of PAEs and APs in the sediments of Taiwanese harbors showed a potential decreasing trend over time, which should be related to strengthened regulations and changes in the industrial market. The estimated total risk quotient (TRQ) of algae exposed to the concentrations of 12 EDCs in sediments suggests moderate to high potential risks (TRQ = 0.74–2.18), while crustaceans (TRQ = 0.02–0.27) and fish (TRQ = 0.03–0.10) may have low to moderate potential risks. The main compounds responsible for these risks are dibutyl phthalate, dioctyl phthalate, and 4-nonylphenols. The results show that the pollution degree of surface sediments in the harbor could reflect anthropogenic pollution. Therefore, it is necessary to monitor the pollution of surface sediments in harbors, grasp the pollution situation, and evaluate the regulatory effect.