To mitigate the environmental hazards of boron mud waste accumulation, we prepared environmental-friendly SiO2 aerogels by extracting them through alkaline leaching treatment and optimized the experimental conditions. The optimum process parameters for alkaline leaching solution NaOH concentration, leaching temperature, solid-to-liquid ratio, and leaching time were 2 mol/L, 95 °C, 1:4, and 3 h, respectively. In this work, cheap and non-toxic hydroxy silicone oil (PDMS–OH) and hydrogen-containing silicone oil (PMHS) were used as surface modifiers instead of toxic and expensive trimethylchlorosilane (TMCS) in the SiO2 aerogel modification process. The best performance under the optimum conditions was achieved with 60% PDMS–OH-modified SiO2 aerogel. Organic liquid spills, represented by toluene, pose a great danger to the environment and water bodies. We treated free toluene on the water surface with the aerogel mentioned above and its adsorption capacity was up to 2,655 mg/g. After the adsorption of toluene, the aerogels coalesced into agglomerates for subsequent collection and handling. Furthermore, after five repeated applications, the adsorption capacity remained at 91.43% of the initial application. Overall, this research provided an inexpensive and simple solution for the treatment of organic liquids in wastewater.