The pervasiveness of microplastics in aquatic ecosystems has become a major environmental issue in recent years. The gradual dumping of plastic wastes, inadequate standard detection methods with specific removal techniques, and slow disposal rate of microplastics make it ubiquitous in the environment. Evidence shows that microplastics act as a potential vector by adsorbing different heavy metals, pathogens, and other chemical additives widely used in different raw plastic production. Microplastics are ingested by aquatic creatures such as fish and different crustaceans, and finally, people ingest them at the tertiary level of the food chain. This phenomenon is responsible for blocking the digestion tracts, disturbing the digestive behavior, finally decreasing the reproductive growth of entire living organisms. Because of these consequences, microplastics have become an increasing concern as a newly emerging potential threat, and therefore, the control of microplastics in aquatic media is required. This paper provides a critical analysis of existing and newly developed methods for detecting and separating microplastics from discharged wastewater, which are the ultimate challenges in the microplastic treatment systems. A critical study on the effect of microplastics on aquatic organisms and human health is also discussed. Thus, this analysis provides a complete understanding of entire strategies for detecting and removing microplastics and their associated issues to ensure a waste discharge standard to minimize the ultimate potential impact in aquatic environments.