Organophosphates are one of the most common pesticides in the world. Among them, one can find malathion that is classified as carcinogenesis, and, as a result, should be appropriately removed since it is highly consumed and possesses a lot of pathogenicity. So far, several processes have been used to remove malathion from aqueous media. The present study investigates its removal by means of Fe3O4 iron oxide nanoparticles. Based on experimental-laboratory studies, using the Response Surface Methodology (RSM), the impact of independent variables such as pH, iron oxide nanoparticle concentration, and contact time on malathion removal efficiency have been investigated. Results show that the pH of the solution is the most important and effective parameter in the process. Optimal conditions of malathion removal based on the appropriate model, obtained from RSM, include 0.4 g/L iron oxide nanoparticles, pH of about 5 (acidic conditions), and contact time of about 1 h with ultraviolet radiation being equal to 82% malathion removal. The process, used in this study, can remove malathion from aqueous solutions according to the so-called conditions, and changing the laboratory conditions can effectively remove it. This process can also be recommended as an economic and scientific method to remove malathion from drinking water.