Purifying polluted water is becoming a crucial concern to meet quantity and quality demands as well as to ensure the resource’s sustainability. In this study, a new material was prepared from cherry stone powder and sodium alginate, and its capacity to remove methylene blue (MB) from water was determined. The characterization of the resulting product, performed via scanning electron microscopy (SEM) and Fourier-transform infrared spectroscopy (FTIR), revealed that the raw material considered for the synthesis was successfully embedded in the polymeric matrix. The impact of three of the main working parameters (pH 3–9, adsorbent dose 50–150 g/L, contact time 60–180 min) on the retention of MB was evaluated through response surface methodology with a Box–Behnken design. In the optimal settings, a removal efficiency of 80.46% and a maximum sorption capacity of 0.3552 mg/g were recorded. MB retention followed the pseudo-second-order kinetic and was suitably described by Freundlich, Khan, Redlich–Peterson, and Sips isotherm models. The experimental results show that the synthesized composite can be used for at least three successive cycles of MB adsorption. From these findings, it can be concluded that the use of the cherry-stone-based adsorbent is environmentally friendly, and efficacious in the removal of contaminants from the water environment.