One of the most important directions for environmental remediation is the effective removal of dyes and toxic heavy metals from water using newly fabricated nanoadsorbents. Here, magnetic Fe3O4 nanoparticles were combined with nitrogen-containing functional group polymers chitosan (CS) and polypyrrole (ppy) to synthesize a nanocomposite (polypyrrole@magnetic chitosan) useful for removing methyl orange (MO) and hexavalent chromium (Cr (VI)) from water. The physicochemical properties of the nanocomposite were determined using SEM, TEM, XRD, FT−IR, and TGA techniques. The effect of different factors on the adsorption system was studied including the contact time, pH, and the effect of co-existed ions. The kinetic study illustrated that the adsorption fit well with Langmuir isotherm. The maximum adsorption capacity of MO and Cr (VI) was found to be 95 and 105 mg/g, respectively. The reusability of the nanocomposite was studied for up to five cycles using 0.1 M NaOH as eluent with a slight decrease of adsorbent efficiency. Furthermore, the removal mechanism studied suggested the removal of MO via adsorption and Cr (VI) via chemical reduction and adsorption. This study suggests that a ppy@magnetic chitosan nanocomposite is a promising nanoadsorbent for removing MO and Cr (VI) from water.