Magnetic nanoparticles (MNPs) have attracted interest on the field of environmental remediation. Similarly, green chemistry has become a topic of interest in recent years because it is a convenient, safe, economic and ecological way of synthesis. The present review shows different sources for the synthesis of MNPs using plant extracts or reduction with biomolecules, as well as the potential applications of these green nanomaterials in remediation tasks, elimination of pollutants from aqueous systems and as an antimicrobial agent. Likewise, the efforts made in the evaluation of the toxicological potential are shown, which show a decrease in the toxicity of these materials compared to those obtained by conventional methods. Finally, the existing gap around the large-scale application of these technologies is discussed.