Fe3O4 magnetic xerogel composites were prepared by polycondensation of resorcinol (R)–formaldehyde reaction via a sol–gel process in an aqueous solution through varying the molar ratio of Fe3O4 nanoparticles (MNPs), catalyst (C), and water (W) content. MNPs were obtained by co-precipitation (MC), oxidation of iron salts (MO), or solvothermal synthesis (MS). Both MNPs and magnetic xerogels were examined regarding the performance of arsenic and fluoride removal in a batch system. The MC-based MNPs had higher adsorption capacities for both fluoride (202.9 mg/g) and arsenic (3.2 mg/g) than other MNPs in optimum conditions. The X-ray diffraction, Fourier transform infrared spectroscopy, and energy-dispersive X-ray spectroscopy confirmed that Fe was composed into the polymeric matrix of magnetic xerogels that contained 0.59%–4.42% of Fe with a molar ratio of MNPs (M) to R between 0.01 and 0.10. With low R/C and optimum M/R ratios, an increase in the surface area of magnetic xerogels affected the fluoride and arsenic adsorption capacities. The magnetic xerogel composites with the MC-based MNPs prepared at a fixed R/C ratio (100) and at different R/W (0.05–0.06) and M/R (0.07–0.10) ratios had a high arsenic removal efficiency of 100% at an As(V) concentration of 0.1 mg/L and pH of 3.0. The maximum adsorption capacities of magnetic xerogels were approximately five times higher than those of the xerogels without MNP composites. Therefore, Fe3O4 nanoparticles enhanced the adsorption of arsenate and fluoride. The variations of alkaline catalyst and water content significantly affected the resulting properties of textural and surface chemistry of magnetic xerogel composites.