For decades, coastal marine ecosystems have been threatened by a wide range of anthropogenic pollutants. Recently, there has been increasing concern about the accumulation and impacts of antibiotic compounds on marine ecosystems. However, information regarding the accumulation of antibiotics and the impacts they may have on microbial communities in coastal water bodies and on human health is sparse in literature. Antibiotics from aquacultures are constantly discharged into marine environments via rivers. Large rivers transport tons of antibiotics every year into coastal waters, e.g., 12 tons of sulfonamide by the river Mekong. Here, we discuss a potential influence of such imported antibiotics on bacterial communities in coastal waters. Potential accumulation of antibiotics in the uppermost surface layer of aquatic ecosystems, the so-called sea surface microlayer (SML), is of interest. Because of the ability of the SML to accumulate anthropogenic pollutants, it may serve as a pool for antibiotics and correspondingly also for resistant organisms. Also, due to its biofilm-like structure, the SML could serve as a hotspot for horizontal gene transfer, speeding up the spread of antibiotic resistant strains to encompassing marine environments. The emergence of antibiotic resistant bacteria is a global threat and scientists projected that it could pave the way for the next pandemic that could ravage the world in the next decades. For this reason, it is time to focus research on understanding and minimizing the impact of antibiotics on the sustainability of coastal waters and on the health of humans who depend on coastal resources for food and recreational purposes. Also, knowledge about antibiotics in the SML is necessary to understand the effects they are likely to have on bacterial abundance, diversity, and metabolic activities in coastal water bodies.