The estuarine ecosystem is under threat due to the addition of different anthropogenic pollutants. Among the various pollutants, microplastics(MPs), and antibiotics play a significant role in affecting estuarine organisms and human health by transport through the food chain. In the estuaries, microorganisms, including pathogens, colonise microplastics by the development of biofilms. Estuaries have long been home to MPs, served as novel hubs for the transmission of Antibiotic Resistance Genes (ARGs). As a result of their continual interactions with a variety of aquatic creatures, MP-associated bacterial communities will eventually present a transfer opportunity to organisms that consume MPs. To comprehend the presence of microplastics and ARGs in the estuaries, a thorough review is necessary. This review discusses the various sources of MPs and antibiotic pollution, as well as the transport of ARGs via biofilm formed on MPs. Furthermore, the factors affecting biofilm formation in estuaries are reviewed. In addition, the transport of ARGs by microbial populations within biofilm is discussed. The ARGs are transported into the food chain, which will be a threat to human health. Hence, the occurrence of antibiotic-resistant genes in fish is discussed.