This study aimed to synthesize Fe3O4 nanoparticles and Pectin/Fe3O4/Bentonite nanocomposite hydrogel. Then this nano adsorbent was used to remove heavy metals (Pb2+, Cu2+, and Ca2+) from aqueous solutions. The percentage of adsorption efficiency for Pb2+, Cu2+, and Cd2+ by 30 mg of adsorbent during 60 minutes and concentration of 200 ppm was 91.5%, 89.5%, and 85%, respectively. At the concentration of 250 ppm, it is 87.2%, 86%, and 80.4%, respectively, and in the concentration of 300ppm, it is 78.66%, 77.33%, and 69%, respectively. In the continuation of the experiment, the optimal conditions for removing heavy metals with nanocomposite under laboratory conditions, pH = 7, contact time of 60 minutes, the concentration of 250 ppm, and adsorbent mass of 0.03 g were carried out. Because the concentration of 250 ppm was considered the average of the other two concentrations. The results of the adsorption isotherm studies exhibit a good fit of the data with the Langmuir adsorption isotherm compared to Freundlich and Temkin models. The collected kinetic and thermodynamics data illustrated that the pseudo-second-order equations, the spontaneous process and endothermic, control the adsorption process.