Mixing the Scenedesmus species with nanoclay and immobilizing in sodium alginate was evaluated as a sustainable treatment method for removing nitrate, atrazine, and metals from groundwater. Gel beads containing the hybrid mixture removed 100% of 10 mg/L N nitrate and 98% of 100 µg/L atrazine from synthetic groundwater in three days. The optimal amount of nanoclay was found to be 0.30 mg per bead. The experimental data fit well into a Freundlich adsorption isotherm and followed pseudo first-order kinetics. When tested in actual groundwater, 91% of nitrate and 100% of Cr, Se, and V were eliminated in three days without need for any nutrients or carbon source. Immobilizing algal beads embedded with nanoclay is a natural, low-cost alternative for groundwater treatment. The gel beads can be reused for at least two cycles without a compromise in performance. They are water-insoluble, easy to harvest, and offer high removal efficiency.