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Water is an essential compound on earth and necessary for life. The presence of highly toxic contaminants such as arsenic and others, in many cases, represents one of the biggest problems facing the earth´s population. Treatment of contaminated water with magnetite (Fe3O4) nanoparticles (NPs) can play a crucial role in arsenic removal. In this report, we demonstrate arsenic removal from an aqueous solution and natural water taken from the Peruvian river (Tambo River in Arequipa, Peru) using magnetite NPs synthesized by the coprecipitation method. XRD data analysis of Fe3O4 NPs revealed the formation of the cubic-spinel phase of magnetite with an average crystallite size of ~ 13 nm, which is found in good agreement with the physical size assessed from TEM image analysis. Magnetic results evidence that our NPs show a superparamagnetic-like behavior with a thermal relaxation of magnetic moments mediated by strong particle-particle interactions. FTIR absorption band shows the interactions between arsenate anions and Fe-O and Fe-OH groups through a complex mechanism. The experimental results showed that arsenic adsorption is fast during the first 10 min; while the equilibrium is reached within 60 min, providing an arsenic removal efficiency of ~ 97%. Adsorption kinetics is well modeled using the pseudo-second-order kinetic equation, suggesting that the adsorption process is related to the chemisorption model. According to Langmuir's model, the maximum arsenic adsorption capacity of 81.04 mg·g− 1 at pH = 2.5 was estimated, which describes the adsorption process as being monolayer, However, our results suggest that multilayer adsorption can be produced after monolayer saturation in agreement with the Freundlich model. This finding was corroborated by the Sips model, which showed a good correlation to the experimental data. Tests using natural water taken from Tambo River indicate a significant reduction of arsenic concentration from 356 µg L− 1 to 7.38 µg L− 1, the latter is below the limit imposed by World Health Organization (10 µg L− 1), suggesting that magnetite NPs show great potential for the arsenic removal. [ABSTRACT FROM AUTHOR]