Nanomaterials possess unique physicochemical properties that position them as promising candidates for environmental remediation, particularly in the removal of persistent organic pollutants (POPs) from aqueous systems. Their high surface area, tunable functionality, and strong adsorption capabilities have attracted significant attention. In this context, this paper reviews the mechanisms of nanomaterial-based POP decontamination, also providing a critical overview of the limitations and challenges in applying these methods. Specifically, issues of stability, reusability, and aggregation are discussed, which can lead to performance decay during repeated use. In addition, the practical application requires nanocomposites to enable efficient separation and mitigate agglomeration. Environmental concerns also arise from nanomaterials' fate, transport, and potential toxicity, which may impact aquatic ecosystems and non-target organisms. When checking for large-scale application feasibility, impurities typically add to production costs, recovery problems, and general infrastructure limitations. In addition to these points, there are no standard guidelines or clear risk assessment procedures for registering a product. Unprecedented cross-disciplinary research between natural, human, and technological studies and outreach programs is needed to facilitate the development and diffusion of the results. The barriers will eventually be breached to move from laboratory success in developing the desperately needed new water purification technologies to field-ready water treatment solutions that can address the global POP contamination problem.