The present study was designed to remove five different direct dyes (Direct Violet 51, Indosol Turquoise FBL, Indosol Black NF, Indosol Yellow BG and Indosol Orange RSN) from aqueous solutions by using agro-industrial waste materials (sugarcane bagasse, peanut husk, corn cobs, cotton sticks and sunflower) in batch and column mode. The batch mode study was performed to compare the biosorption potential of native, pretreated and immobilized forms of biosorbents for the removal of direct dyes. Important process parameters like pH, contact time, biosorbent dose, initial dye concentration and temperature were optimized during batch experiments. The results revealed that low pH, low biosorbent dose and low temperature were the feasible conditions for maximum removal of dyes. The pretreated form of biosorbents depicted highest biosorption capacity (39.6 mg/g for Direct Violet 51, 65.09 mg/g for Indosol Turquoise FBL, 89.6 mg/g for Indosol Black NF, 79.5 mg/g for Indosol Yellow BG and 79.7 mg/g for Indosol Orange RSN) as compare to native and immobilized form of biosorbents. The experimental data of all the five dyes was subjected to different kinetic models and pseudo-second order kinetic model was found to be best fit on the experimental results. Different equilibrium isotherms were applied on the data to explain the mechanism of biosorption and Langmuir adsorption isotherm model fitted very well on the experimental results for all the dyes. Thermodynamic study showed that biosorption process was feasible at lower temperatures as indicated by lower values of ∆G. The negative values of ∆H indicated that biosorption process was exothermic in nature. The column mode experiments were conducted to optimize the bed height, flow rate and initial dye concentration. Higher bed heights, lower flow rates and higher initial dye concentrations were found to be favorable conditions for maximum dye removal in column mode study. Box-Behnken experimental design was used to investigate the main and interaction effects of three important parameters like initial dye concentration, biosorbent dose and pH on the removal of direct dyes and results were analyzed by ANOVA and p-values. The biosorption process was also applied on the real textile effluents for the efficient removal of COD. Characterization of biosorbents was carried out by FT-IR and SEM analysis. The results revealed that agricultural waste materials have high biosorption capacities for the removal of dyes from wastewaters.