The proliferation of antibiotic resistance in marine ecosystems represents a critical One Health challenge, particularly within coastal habitats that receive anthropogenic inputs. This study presents an integrative, multi‑media assessment of 50 antibiotics alongside intracellular and extracellular antibiotic resistance genes (iARGs and eARGs) across three ecologically significant marine protected areas (MPAs) in the South China Sea. These MPAs are designated as National Aquatic Germplasm Resources Reserves, serving as critical habitats for important species and playing a vital role in regional marine biodiversity conservation. We quantified contaminants across dissolved, suspended particulate, and sedimentary phases during dry and wet seasons. Total antibiotic concentrations were highest in the dry season, ranging 97.60−312.18 ng/L (dissolved), 18.61–34.56 ng/L (particulate), and 27.62–115.48 ng/g dry weight (sediment). Correspondingly, the absolute abundance of iARGs (2.99×10⁶−1.73×10⁸ copies/g) exceeded that of eARGs (2.36×10⁵−4.89×10⁷ copies/g) in the dry season, with both antibiotic and ARG levels elevated relative to the wet season. Variation partitioning analysis revealed that environmental factors (e.g., dissolved oxygen and salinity) and heavy metals (e.g., Hg, Cu, Zn, and Cr) independently explained 47% and 38% of the total variance in ARG profiles, respectively, indicating heavy metals act as important co-selective pressures. Overall, this study highlights the pivotal roles of hydrodynamic conditions and metal co-contamination in shaping the dissemination risk of antibiotic resistance within protected nearshore ecosystems. By demonstrating spatiotemporal patterns and dominant drivers, this work provides a critical evidence base for designing targeted surveillance and mitigation strategies to safeguard ecological health in MPAs facing increasing anthropogenic stress.