The present research focuses on the application of peanut and walnut shells, in their natural state, for the removal of methylene blue (MB) from water solutions in batch and dynamic (flow-through) conditions. Under batch conditions, at a 100 mg/L MB concentration of aqueous solution, the optimum dose of the studied biosorbents was determined to be 2.5 g/L, reaching about 95–97% efficiency of MB removal for both materials. Langmuir and Freundlich isotherms were used to model and evaluate the experimental data under different initial concentrations of MB (25 to 100 mg/L). The determined maximum adsorption capacities are 41.50 mg/g for walnut shells and 46.80 mg/g for peanut shells. Under flow-through conditions, breakthrough curves are determined for three sizes of fractions (<0.25 mm, 0.315–0.5 mm, and 0.8–1.6 mm). For peanut shells, the smaller the particle size, the higher the adsorption capacity and the column breakthrough time. For walnut shells, however, the particle size seems to have a more complex influence on the adsorption process parameters, and this phenomenon deserves future investigation. The adsorption capacity for one and the same fraction size of 0.315–0.5 mm and initial MB concentration of 50 mg/L is higher under dynamic flow conditions, i.e., 51 mg/g compared to 20 mg/g for walnut shells and 46 mg/g compared to 17.5 mg/g for peanut shells.