Water is an important component of life and plays a vital role in human and animal lives, and because of these essential roles of water to life, access to quality water and in adequate quantity becomes imperative. Subsequently, water/wastewater systems have become established as reservoirs of antimicrobial resistance determinants in the environment. In this study, we carried out the synthesis and characterization of magnetite nanoparticles for use in the removal of genomic DNA of antibiotic resistant Escherichia coli isolate in aqueous system. The synthesis of this nanoparticle was achieved by using precipitation method and characterization of the material was conducted by using Fourier transform infrared spectroscopy (FTIR), scanning electron spectroscopy (SEM), electron diffraction spectroscopy (EDS), and vibrating sample magnetometry (VSM). The SEM analysis revealed that this material is spherical in shape, while the FTIR spectra revealed Fe–O vibrational band at ~ 450 cm−1 confirming the success of the synthesis of this material. The magnetite nanomaterial showed efficiency for the removal of the bacterial DNA from water with a maximum removal capacity of 45.5 ng g−1. The effect of pH (qe max = 55 ng g−1 @ pH = 10), time (qt max @ 180 min), DNA concentration (DNA concentration of 185 ng/mL, qe max = 45.5 ng g−1), and adsorbent weight (% adsorption max = 61.65% @ 0.025 g) suggest that adsorption conditions influence the removal of DNA by this material. In addition, kinetic study shows that the removal of bacterial DNA obeyed pseudo 2nd order indicating that adsorption process was achieved by bimolecular interaction between magnetite and antibiotics resistant bacterial DNA. We conclude that magnetite nanoparticle appears to be a potential candidate for the removal of nucleic acids and antimicrobial resistance determinants in water/wastewater treatment.