Globally, freshwater is insufficiently distributed to meet all present and future water demands. As a result, agricultural water demands must be satisfied by creative methods such as wastewater treatment and recycling. Several physical and chemical remediation procedures have been utilised to degrade or remove environmental pollutants in wastewater. Some techniques produce toxic metabolites, are ecologically unfriendly and expensive, or entail the relocation of contaminants rather than reducing them. It is, therefore, critical to incorporate biological approaches that use organisms’ metabolic activities to break down or change toxic contaminants into less dangerous intermediates or products. Employing plant symbiont microorganisms known as endophytes has been shown as a sustainable and eco-friendly approach for decontaminating water and enhancing agricultural output. In this chapter, we highlight the potential of endophytes as wastewater bioremediation, biotransformation, and disinfection agents.