A helical module microchannel reactor (MR) was developed for the preparation of magnetic iron oxide nanoparticles (MIONPs) by co-precipitation. The product properties were characterized by TEM, XRD, XPS and BET, which showed that the MIONPs obtained from MR appeared a more uniform size distribution, a better crystallinity, a smaller size but larger specific surface area, as compared to their counterpart obtained from conventional stirred reactor (SR). The workability of the synthesized MIONPs using MR in waste water treatment was examined using aqueous arsenite, arsenate and chromate as samples. The results obtained in the present study showed the advantages of using MR to fabricate MIONPs with high conversion yield and high productivity. The fabricated MIONPs is promising for a rapid and complete removal of aqueous hazard compounds.