A semi-enclosed bay as a pharmaceutical hotspot and an open strait as a regional reservoir: Contrasting pharmaceuticals and antibiotic resistance

Pharmaceuticals and antibiotic resistance genes (ARGs) are increasingly recognized as emerging pollutants in coastal ecosystems, yet their contrasting behaviors in open straits versus semi-enclosed bays remain poorly understood. Here, we determined their concentrations across various sampling sites and seasons, together with mobile genetic elements (MGEs), in different water layers of the western Taiwan Strait and Dongshan Bay. In the Taiwan Strait, pharmaceutical concentrations were relatively low (0.60–81.20 ng/L), yet ocean currents may have played a pivotal role in redistributing both chemical and genetic pollutants. Despite the absence of corresponding antibiotics, multiple ARG classes (multidrug, aminoglycoside, MLSB) persisted, with strong correlations to transposase genes, underscoring the overlooked role of offshore waters as active reservoirs for horizontal gene transfer. In sharp contrast, Dongshan Bay—especially intensive aquaculture zones—exhibited substantially higher pharmaceutical levels (29.34–174.52 ng/L) and 74 ARGs dominated by multidrug resistance. Integrons ( intI1 ) were tightly linked to diverse ARG classes, and ARG abundance correlated positively with antibiotic concentrations, directly implicating mariculture and terrestrial inputs as key drivers of resistance enrichment. Collectively, our findings reveal that semi-enclosed bays are vulnerable accumulators of anthropogenic contamination, while offshore straits serve as active pathways for pollutant redistribution and resistance propagation. • Pharmaceuticals, ARGs, and MGEs were compared in strait and bay systems. • Diclofenac, a non-antibiotic drug, was present at the highest concentration. • Hydrodynamics probably redistribute pollutants and sustain ARGs in the open strait. • Aquaculture and land inputs enrich ARGs via integron transfer in the bay.