Naturally abundant and renewable macromolecular polysaccharides are now considered as green and sustainable adsorbent material for toxic effluent treatment. However, to deal with complex wastewater, the need for efficient amphoteric adsorbent is still a challenge. Herein a three-dimensional (3D) composite aerogel is prepared from dodecyl amine modified clay (kaolinite) enriched chitosan/alginate via freeze drying method and a post ionic crosslinking. The aerogel was characterized by Fourier transform infrared spectroscopy (FT-IRS), scanning electron microscopy (SEM), energy dispersive X-ray (EDX), thermogravimetric analysis (TGA), X-ray diffraction (XRD), solubility test and adsorption studies. The thermal stability of aerogel was significantly higher than that of chitosan/alginate polymer matrix and substantially increased upon gradual addition of modified clay. The aerogel has ordered fishing net-like microstructure, and interconnected pores for dyes and metal ions adsorption. The adsorption capacities of composite aerogel on methylene blue, acid black and hexavalent chromium [Cr (VI)] ions was reached around 73.1, 71.5, and 62.4 mg/g respectively. The adsorption mechanism was electrostatic interaction and the mass ratio of chitosan and modified clay to alginate regulate the adsorption capacities for the anionic and cationic dyes. As a novel amphoteric adsorbent, the chitosan/alginate/modified clay composite aerogel showed the potential to remove both cationic, anionic dyes and metal ions from wastewaters. Moreover, the prepared biobased aerogel showed high adsorption efficiency in both acidic and basic media even after four cycles. The study demonstrated a high performance, low cost, with materials locally available, recyclable and promising candidate for industrial waste water treatment.