Natural adsorbents as low-cost materials have been proved efficient for water remediation and have significant capacity for the removal of certain chemicals from wastewater. The present investigation aimed to use Citrullus colocynthis seeds (CCSs) and peels (CCPs) as an efficient natural adsorbent for methylene blue (MB) dye in an aqueous solution. The examined biosorbents were characterized using surface area analyzer (BET), scanning electron microscope (SEM), thermogravimetric analyzer (TGA) and Fourier transform infra-red (FT-IR) spectroscopy. Batch adsorption experiments were conducted to optimize the main factors influencing the biosorption process. The equilibrium data for the adsorption of MB by CCSs were best described by the Langmuir isotherm followed by the Freundlich adsorption isotherms, while the equilibrium data for MB adsorption by CCPs were well fitted by the Langmuir isotherm followed by the Temkin isotherm. Under optimum conditions, the maximum biosorption capacity and removal efficiency were 18.832 mg g−1 and 98.00% for MB-CCSs and 4.480 mg g−1 and 91.43% for MB-CCPs. Kinetic studies revealed that MB adsorption onto CCSs obeys pseudo-first order kinetic model (K1 = 0.0274 min−1), while MB adsorption onto CCPs follows the pseudo-second order kinetic model (K2 = 0.0177 g mg−1 min−1). Thermodynamic studies revealed that the MB biosorption by CCSs was endothermic and a spontaneous process in nature associated with a rise in randomness, but the MB adsorption by CCPs was exothermic and a spontaneous process only at room temperature with a decline in disorder. Based on the obtained results, CCSs and CCPSs can be utilized as efficient, natural biosorbents, and CCSs is promising since it showed the highest removal percentage and adsorption capacity of MB dye.