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Emerging pollutants are hazardous to the ecological environment and human health, and these issues have attracted increasing attention from scholars. In the current study, the Taiwan Strait is long and narrow, highly influenced by terrestrial domains, and frequently disturbed by human activities. Conversely, the Luzon Strait is an open sea far from the shore, and the impact of human activities on it is minimal. The description of antibiotics in two different types of seas revealed that contaminants were most commonly detected in both straits. In particular, the coasts of the Minjiang River, Jinjiang River, and Jiulong River were found to be pollution hotspots in the Taiwan Strait. The calculation of risk quotients revealed that antibiotics were more sensitive to algae. Furthermore, estimation of the risk quotients of the mixtures found that antibiotics in the environment do not pose a high risk to aquatic organisms at different trophic levels. • Antibiotics showed significant differences between Taiwan Strait and Luzon Strait. • Taiwan Strait was highly influenced by human activities and terrestrial domains. • Minjiang River contributed dominantly input flux of antibiotics into Taiwan Strait. • Tetracyclines and fluoroquinolones posed more sensitive risk to algae in both straits [ABSTRACT FROM AUTHOR]