Addressing the critical issue of water pollution, this review article emphasizes the need to remove hazardous dyes and phenolic compounds from wastewater. These pollutants pose severe risks due to their toxic, mutagenic, and carcinogenic properties. The study explores various techniques for the remediation of organic contaminants from wastewater, including an enzymatic approach. A significant challenge in enzymatic wastewater treatment is the loss of enzyme activity and difficulty in recovery post-treatment. To mitigate these issues, this review examines the strategy of immobilizing enzymes on newly developed nanostructured materials like graphene, carbon nanotubes (CNTs), and metal–organic frameworks (MOFs). These materials offer high surface areas, excellent porosity, and ample anchoring sites for effective enzyme immobilization. The review evaluates recent research on enzyme immobilization on these supports and their applications in biocatalytic nanoparticles. It also analyzes the impact of operational factors (e.g., time, pH, and temperature) on dye and phenolic compound removal from wastewater using these enzymes. Despite promising outcomes, this review acknowledges the challenges for large-scale implementation and offers recommendations for future research to tackle these obstacles. This review concludes by suggesting that enzyme immobilization on these emerging materials could present a sustainable, environmentally friendly solution to the escalating water pollution crisis.