Super-paramagnetic iron-oxide nanoparticles (SPIONs) have been exploited from a very long time and are researched profoundly due to their unique properties. In this study, SPIONs were synthesized using environmentally accepted green synthesis process where Azadirachta indica leaf extract was used as one of the reducing agents along with basic metal precursors used in chemical processes. The synthesized SPIONs were characterised using microscopic analysis (SEM, TEM, and AFM), spectroscopic analysis (FT-IR, UV–Vis, XRD, Raman, and zeta potential), and magnetometry (SQUID). The SPIONs were then tested for its application in the removal of heavy metals from tannery waste water and also X-ray imaging.