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Nano-porous aerogels are an advantageous approach to produce low-density materials with high surface area, particularly when using biobased materials. Frequently, most biobased aerogels are synthesized through a bottom-up approach, which requires high energy inputs to break and rebuild the raw materials, and for elimination of water. To curb this, this work focused on generating aerogels by a top-down approach through the delignification of a wood substrate while eliminating water by solvent exchange. To diversify the surface chemistry for use in water treatment, the delignified wood–nanowood-was coated with a chitosan–cyclodextrin co-polymer and tested in the capture of microcystin-LR. The generated nanowood structure had 75% porosity after coating, with up to 339% water swelling and an adsorption capacity of 0.12 mg g −1 of the microcystin. This top-down technique enables the generation of low-cost aerogels by reducing steps, using a biobased self-assembled coating with hydrophobic active sites, and avoiding costly energetic input.