The increase in production in the chemical manufacturing industry has led to high levels of waste generated as a byproduct. Inadequate waste management has resulted in water pollution by micropollutants, such as bisphenol A (BPA). BPA, as an endocrine-disrupting compound, has various negative effects on human health and aquatic environments. BPA adsorption using mesoporous silica (MS) can be an economic and efficient solution to overcome this problem. However, MS is typically synthesized using tetraethyl orthosilicate (TEOS), which is toxic and expensive. Therefore, this study explores the use of geothermal silica scaling as an environmentally friendly source of silica for MS synthesis. The sol–gel process was modified using a sonochemical approach, and the effect of the sonication time on MS characteristics was analyzed. The results showed that increasing the sonication time affected the growth of the regular meso-sized pore structure, with a sonication time of 30 min (MS-US 30) producing MS with optimal pore and surface properties. MS-US 30 has a hexagonal structure, with a specific surface area of 181 m2 g−1, pore size of 3.79 nm, and pore volume of 0.18 cm3 g−1. MS-US 30 showed promising adsorption performance against BPA, with a removal efficiency and adsorption capacity of up to 64.94% and 194.81 mg g−1, respectively, within a contact time of 3 h at a pH of 10. The synthesis of MS from geothermal silica scaling provides a sustainable approach to MS synthesis, showing reliable adsorption performance and potential for further development. These findings also suggest that sonication-assisted synthesis offers a more efficient and favorable alternative route for MS synthesis. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.