Serious environmental and health problems arise from the everyday release of industrial wastewater effluents. A wide range of pollutants, such as volatile organic compounds, heavy metals or textile dyes, may be efficiently removed by silica materials advanced solutions such as aerogels. This option is related to their exceptional characteristics that favors the adsorption of different contaminants. The aerogels performance can be selectively tuned by an appropriate chemical or physical modification of the aerogel’s surface. Therefore, the introduction of amine groups enhances the affinity between different organic and inorganic contaminants and the silica aerogels. In this work, different case studies are reported to investigate and better understand the role of these functional groups in the adsorption process, since the properties of the synthesized aerogels were significantly affected, regarding their microstructure and surface area. In general, an improvement of the removal efficiency after functionalization of aerogels with amine groups was found, with removal efficiencies higher than 90% for lead and Rubi Levafix CA. To explain the adsorption mechanism, both Langmuir and Freundlich models were applied; chemisorption is most likely the sorption type taking place in the studied cases.