The phenomenon of water pollution as a consequence of the release of herbicides and pesticides into the environment is an outgrowing problem that requires performing and regenerable adsorbent materials. This work presents the synthesis of a nanocrystalline silicon carbide aerogel and its application in removing glyphosate from polluted water. The aerogel was synthesized via Polymer-Derived Ceramic (PDC) route using allylhydridopolycarbosilane as polymeric precursor. By pyrolysis at 1500 °C in argon, the crystallization of β-SiC nanocrystals was observed, while the aerogel preserved a high specific surface area of 215 m2·g−1. The nanostructured aerogel was tested for glyphosate herbicide, showing a remarkable adsorption of 0.607 mg·g−1, being the initial glyphosate concentration of 2 mg·L−1, and a removal of 93% of the pollutant in solution. Elovich kinetics adsorption and Langmuir isotherm models were found to be the most suitable to describe the mechanism of glyphosate capture via adsorption onto the aerogel surface.