Hazardous chemicals like toxic organic dyes are very harmful to the environment and their removal is quite challenging. Therefore there is a necessity to develop techniques, which are environment friendly, cost-effective and easily available in nature for water purification and remediation. The present research work is focused on the development` and characterization of the ecofriendly semi-interpenetrating polymer network (semi-IPN) nanocomposite hydrogels composed of polyvinyl alcohol (PVA) and alginate (Alg) hydrogel beads incorporating natural bentonite (Bent) clay as a beneficial adsorbent for the removal of toxic methylene blue (MB) from aqueous solution. PVA−Alg/Bent nanocomposite hydrogel beads with different Bent content (0, 10, 20, and 30 wt%) were synthesized via external ionic gelation method. The designed porous and steady structure beads were characterized by the use of Fourier transform infrared spectroscopy (FTIR), energy-dispersive X-ray spectroscopy (EDX), and scanning electron microscopy (SEM). The performance of the beads as MB adsorbents was investigated by treating aqueous solutions in batch mode. The experimental results indicated that the incorporation of Bent (30 wt%) in the nanocomposite formulation sustained the porous structure, preserved water uptake, and increased MB removal efficiency by 230% compared to empty beads. Designed beads possessed higher affinity to MB at high pH 8, 30 °C, and fitted well to pseudo-second-order kinetic model with a high correlation coefficient. Moreover, the designed beads had good stability and reusability as they exhibited excellent removal efficiency (90%) after six consecutive adsorption-desorption cycles. The adsorption process was found be combination of both monolayer adsorption on homogeneous surface and multilayer adsorption on heterogeneous surface. The maximum adsorption capacity of the designed beads system as calculated by Langmuir isotherm was found to be 51.34 mg/g, which is in good agreement with the reported clay-related adsorbents. The designed semi-IPN PVA−Alg/Bent nanocomposite hydrogel beads demonstrated good adsorbent properties and could be potentially used for MB removal from polluted water.