The present work reports an efficient removal of a cationic dye, methylene blue (MB), and an anionic dye, methyl orange (MO) dye from an aqueous solution using graphene oxide (GO)–based nanocomposite as an adsorbent. GO was investigated as a potential nano-reinforcing filler in starch/poly(vinyl alcohol) (PVA) biopolymer matrix. Bio-nanocomposite based on starch/PVA matrix and GO were prepared by an aqueous casting method. The fabricated nanocomposites were characterized using FT-IR, XRD, Raman, TEM, FE-SEM, tensile study, Brunauer–Emmett–Teller (BET) method, Barrett–Joyner–Halenda (BJH) method, zeta potential, and swelling study. The effect of the various compositions of GO nanofiller in the starch/PVA matrix was highlighted and the impact of GO nanosheets on the properties of the nanocomposites was revealed. The results demonstrated that the starch/PVA matrix with 3 g of GO was found to be the optimal concentration of GO. Batch adsorption experiments were conducted to optimize the operational factors, including adsorbent dosage, pH, and contact time, which were systematically investigated. The kinetics of adsorption followed a pseudo-second-order model, while the Langmuir isotherm model described the equilibrium adsorption capacity. The prepared nanocomposite exhibited a maximum monolayer adsorption capacity of 382 mg g−1 for MB dye and 293.3 mg g−1 for MO dye. Based on the calculated thermodynamic parameters for the adsorption of MB (∆H° = − 16.37 kJ mol−1, ∆S° = − 37.99 J K−1 mol−1 and ∆G° from − 4.39 to − 5.13 kJ mol−1) and MO (∆H° = − 13.72 kJ mol−1, ∆S° = − 31.78 J K−1 mol−1 and ∆G° from − 3.72 to − 4.39 kJ mol−1) dyes onto the nanocomposite material was feasible, exothermic, and spontaneous. A plausible adsorption mechanism was proposed, involving electrostatic attraction, H-bonding, and π-π interactions, which collectively governed the adsorption process. The nanocomposite showed good stability and reusability up to five cycles for the uptake of MB and MO dyes. These findings confirmed the effectiveness of the proposed approach to produce bionanocomposite with enhanced properties, which may be used in water purification technology.